When creating a tunnel/ link between two sites and site (A) ISP modem has 1500 mtu (server) and site (B) client has mtu 1492, how to you configure the setting between them/on each one?

For example, on L2TP/Ipsec or GRE/Ipsec do you remove 28 and 24 respectively and add them on each site (meaning e.g., L2TP/Ipsec site (A) mtu 1472 and for site (B) 1464 – GRE/Ipsec site (A) mtu 1476 and for site (B) 1468), or do you follow the “Server” setting (for L2TP) and add 1500 for Server and 1472 for site (B) client?

Thank you in advance !

In principle MTU is end-to-end property of a connection. So you should set it to lowest number known to exist on a connection, in your case it would be 1492 gross (and substract tunnel overhead from that). It may happen that even this setting is too big if there's an intermediate segment of the connection with even lower MTU (nowdays not very likely but possible), in this case there will be further fragmentation.

It can happen that MTU is not the same in both directions (specially so if intermediate links are not symmetrical, so packets traverse different links in both directions), in this case you would have asymmetrical MTU settings on your tunnel. This is not very common though so usually one should stick to rule I wrote in previous paragraph.