Yes, it can also affect the SYN/ACK. The SYN/ACK packet contains no data, so it will be smaller than 1320 bytes anyway.
During the TCP handshake, both the client and the server advertise MSS values in the SYN and SYN/ACK packets to inform the peer of the maximum segment size (MSS) they are able to accept. To avoid packet fragmentation, the MSS value must not exceed the MTU on the communication path.
Example if your MTU is set to 1320:
1a) Client sends SYN with MSS 1460
1b) Firewall changes the (MTU 1320 - IP header - TCP header) to MSS size1280
2a) Server replies with SYN/ACK MSS 1280 or 1460 (old stacks)
2b) Firewall/povider router changes - it if necessary - here also to MSS size 1280
Handshake packets itself are normally not reduced in relevant way. The negotiated maximum segment size is reduced. This has then effect on the following data traffic. If the line can handle this only smaller in direction to the firewall, then maybe the router at provider side must/should do this and also set the MSS to 1280.
However, since this only applies to TCP, you can't use it with UDP or other protocols anyway, because fragmentation comes into play there.
Because you're dealing with the external interface, I think this refers to the connection to the provider. I would always try to set up a connection with an MTU of 1500 (1460 for data). Otherwise, your internet connection will keep slowing down because of MSS (TCP) or fragmentation (UDP), which makes the connection slower and slower.
➜ CCSM Elite, CCME, CCTE ➜ www.checkpoint.tips