Hey, yeah I would be glad if you could shed some light on this.
The hardware switch config at least interferres with the bond, any other setting does not work. I expected to end up with an untagged bond, but the vlan on the bond interface seems to act as a default vlan. The initial configuration is 3-4 years old an was migrated to a newer firmware, "bridge vlans" didn't exist when that router was setup, but I wasn't sure if it is worth migrating?
EDIT: I think what I did is the discouraged
VLAN in bridge with a physical interface
1 is the internet
2 and 6 are trunks to an switch
3+4 is the bond
# dec/19/2020 02:05:09 by RouterOS 6.44.3
# software id = TQ36-1UAQ
#
# model = 2011UiAS-2HnD
# serial number = XXXX
/interface bridge
add admin-mac=5C:4B:2B:1C:72:A0 auto-mac=no comment=defconf name=bridge
add name=bridge-vlan-dmz-20
add name=bridge-vlan-guest-80
add name=bridge-vlan-int-40
/interface ethernet
set [ find default-name=ether1 ] name=eth01-outside speed=100Mbps
set [ find default-name=ether2 ] name=eth02-master speed=100Mbps
set [ find default-name=ether3 ] name=eth03 speed=100Mbps
set [ find default-name=ether4 ] mac-address=6C:3B:6B:8C:7D:A1 name=eth04 speed=100Mbps
set [ find default-name=ether5 ] name=eth05 speed=100Mbps
set [ find default-name=ether6 ] advertise=10M-half,10M-full,100M-half,100M-full,1000M-half,1000M-full name=eth06-master
set [ find default-name=ether7 ] advertise=10M-half,10M-full,100M-half,100M-full,1000M-half,1000M-full name=eth07
set [ find default-name=ether8 ] advertise=10M-half,10M-full,100M-half,100M-full,1000M-half,1000M-full name=eth08
set [ find default-name=ether9 ] advertise=10M-half,10M-full,100M-half,100M-full,1000M-half,1000M-full name=eth09
set [ find default-name=ether10 ] advertise=10M-half,10M-full,100M-half,100M-full,1000M-half,1000M-full name=eth10
set [ find default-name=sfp1 ] disabled=yes
/interface wireless
set [ find default-name=wlan1 ] country=switzerland disabled=no distance=indoors frequency=2467 frequency-mode=regulatory-domain installation=indoor mode=ap-bridge name=wlan-int-40 ssid="Internal WLAN" vlan-id=40 wireless-protocol=802.11 \
wps-mode=disabled
add disabled=no keepalive-frames=disabled mac-address=6E:3B:6B:8C:7D:AA master-interface=wlan-int-40 multicast-buffering=disabled name=wlan-iot-40 ssid="IOT WLAN" vlan-id=40 wds-cost-range=0 wds-default-cost=0 wps-mode=disabled
/interface vlan
add interface=bridge name=vlan-dmz-20 vlan-id=20
add interface=bridge name=vlan-guest-80 vlan-id=80
add interface=bridge name=vlan-int-40 vlan-id=40
/interface bonding
add arp=disabled mode=802.3ad name=bond-nas-34 slaves=eth03,eth04
/interface vlan
add interface=bond-nas-34 name=vlan-int-bond vlan-id=40
/interface ethernet switch port
set 2 default-vlan-id=1 vlan-header=add-if-missing vlan-mode=secure
set 5 default-vlan-id=40 vlan-header=always-strip vlan-mode=secure
set 6 default-vlan-id=1 vlan-header=add-if-missing vlan-mode=secure
set 7 default-vlan-id=1 vlan-header=add-if-missing vlan-mode=secure
set 8 default-vlan-id=40 vlan-header=always-strip vlan-mode=secure
set 9 default-vlan-id=20 vlan-header=always-strip vlan-mode=secure
set 10 default-vlan-id=80 vlan-header=always-strip vlan-mode=secure
set 11 vlan-mode=check
set 12 vlan-mode=check
/interface list
add exclude=dynamic name=discover
add name=mactel
add name=mac-winbox
/interface wireless security-profiles
set [ find default=yes ] authentication-types=wpa2-psk eap-methods="" mode=dynamic-keys supplicant-identity=MikroTik wpa-pre-shared-key="xxx" wpa2-pre-shared-key="xxx"
add authentication-types=wpa2-psk eap-methods="" mode=dynamic-keys name=profile-guest supplicant-identity=MikroTik wpa-pre-shared-key="xxx" wpa2-pre-shared-key="xxx"
add authentication-types=wpa-psk,wpa2-psk eap-methods="" management-protection=allowed mode=dynamic-keys name=hotspot supplicant-identity="" wpa-pre-shared-key="xxx" wpa2-pre-shared-key="xxx"
/interface wireless
add disabled=no mac-address=6E:3B:6B:8C:7D:A9 master-interface=wlan-int-40 name=wlan-guest-80 security-profile=profile-guest ssid="Guest WLAN" vlan-id=80 wps-mode=disabled
/interface bridge filter
add action=drop chain=forward in-interface=wlan-guest-80
add action=drop chain=forward out-interface=wlan-guest-80
/interface bridge port
add bridge=bridge comment=defconf interface=eth02-master
add bridge=bridge-vlan-int-40 comment=defconf interface=wlan-int-40
add bridge=bridge interface=eth06-master
add bridge=bridge-vlan-int-40 interface=vlan-int-40
add bridge=bridge-vlan-guest-80 interface=vlan-guest-80
add bridge=bridge-vlan-guest-80 interface=wlan-guest-80
add bridge=bridge-vlan-dmz-20 interface=vlan-dmz-20
add bridge=bridge interface=eth10
add bridge=bridge interface=eth05
add bridge=bridge interface=eth07
add bridge=bridge interface=eth08
add bridge=bridge interface=eth09
add bridge=bridge-vlan-int-40 interface=bond-nas-34
add bridge=bridge-vlan-int-40 disabled=yes interface=eth03
add bridge=bridge-vlan-int-40 disabled=yes interface=eth04
/interface bridge settings
set use-ip-firewall-for-vlan=yes
/interface ethernet switch vlan
add ports=eth06-master,eth07,eth08,switch2-cpu switch=switch2 vlan-id=40
add ports=eth06-master,eth07,eth10,switch2-cpu switch=switch2 vlan-id=80
add independent-learning=no ports=eth02-master,eth05,switch1-cpu switch=switch1 vlan-id=40
add independent-learning=no ports=eth02-master,switch1-cpu switch=switch1 vlan-id=80
add ports=eth06-master,eth09,switch2-cpu switch=switch2 vlan-id=20
add independent-learning=no ports=eth02-master,switch1-cpu switch=switch1 vlan-id=20
/interface list member
add interface=sfp1 list=discover
add interface=eth02-master list=discover
add interface=eth03 list=discover
add interface=eth04 list=discover
add interface=eth05 list=discover
add interface=eth06-master list=discover
add interface=eth07 list=discover
add interface=eth08 list=discover
add interface=eth09 list=discover
add interface=eth10 list=discover
add interface=wlan-int-40 list=discover
add interface=bridge list=discover
add interface=vlan-int-40 list=discover
add interface=vlan-guest-80 list=discover
add interface=bridge-vlan-int-40 list=discover
add interface=bridge-vlan-guest-80 list=discover
add interface=wlan-guest-80 list=discover
add interface=vlan-dmz-20 list=discover
add interface=bridge-vlan-dmz-20 list=discover
add interface=eth02-master list=mactel
add interface=eth06-master list=mactel
add interface=eth02-master list=mac-winbox
add interface=eth10 list=mactel
add interface=eth06-master list=mac-winbox
add interface=sfp1 list=mactel
add interface=eth10 list=mac-winbox
add interface=wlan-int-40 list=mactel
add interface=sfp1 list=mac-winbox
add interface=wlan-guest-80 list=mactel
add interface=wlan-int-40 list=mac-winbox
add interface=wlan-guest-80 list=mac-winbox