Hi
I have a number of separate networks for separate customers across different physical addresses.

I would like to be able to send out an access point that can be plugged in on site and is pre-configured to communicate back to a central capsman server via the internet.
Much like I can do with unifi. It gets an ip/gateway/dns via dhcp and then calls home to our unifi server to download its ssid/pass configuration.

In the unifi controller, i can create various customer "sites" and each has its own ssid and password. All access points under a site send only their usage statistics back to the unifi controller.

Can I create multiple independent sites on the capsman server?
I was told, and i could be wrong about this, but capsman routes the customer traffic via the capsman server. Can anyone confirm if this is true?

I dont want the customer traffic routed back to the capsman server, and i want each customer site to have its own ssid/wpa2password without having to run multiple capsman servers or a capsman server at each customer site.

Your help is very much appreciated.

I haven't worked with ubiquity controller, but from what I've heard they have slightly different logic compared to capsman. Ubiquity controller is used only for downloading settings and then the point can work without it
In capsman wifi interface is passed under the control of the controller. The controller is engaged in authorization of clients (due to which the time of transition from one point to another is reduced, as re-authorization is not necessary).
That is, most of the work of the wifi network is done by Kapsman, and when it is disconnected, all points stop working.
For remote management of statistics and status monitoring is used another product Mikrotika free programs Dude.
Now the answers to your questions

I would like to be able to send out an access point that can be plugged in on site and is pre-configured to communicate back to a central capsman server via the internet.

Yes. But they don't usually do that

Can I create multiple independent sites on the capsman server?

Yes you can create many different combinations of SSIDs and passwords

I was told, and i could be wrong about this, but capsman routes the customer traffic via the capsman server. Can anyone confirm if this is true?

Yes and no.
Traffic is split into two parts. Service traffic related to wifi operation necessarily goes through the capsman controller.
User data traffic is routed locally by the access point or centrally by the capsman.

I was told, and i could be wrong about this, but capsman routes the customer traffic via the capsman server. Can anyone confirm if this is true?

Yes and no.
Traffic is split into two parts. Service traffic related to wifi operation necessarily goes through the capsman controller.
User data traffic is routed locally by the access point or centrally by the capsman.

On that last part about user traffic, it depends which wifi version is being used for capsman/caps.
Legacy wifi: you are correct.
wifiwave2: only local forwarding by access point. Central forwarding is not (yet ?) supported.