Yes, it's compatible at the moment. However, I'd need Kara to confirm the details, but I'm not sure just how much the whole FSNET2 is going to change.
Basically, we are trying to promote the SCP, features and all, and the more people are playing on Toms build the less people are actually testing the SCP to get rid of those bugs. If another version of Toms build comes out, it may well simply be that those problems will get transferred on to another generation.
Personally, I'd much rather people actually helped the SCP guys fix the bugs in the main and supported version so that everyone can play multiplayer than having multiple versions of Freespace 2 knocking around with different SexP's and feature support. It actually makes the coders' job a lot harder, and also makes expanding the abilities of SCP Multiplay to support new game modes etc a lot harder as well.
Toms build was a great addition at the time, the multiplayer support for Freespace hadn't been touched that much and it allowed people to play online again, but we need to move on from it, I don't want it to become a ball and chain around the ankle of the SCP, The whole purpose of the SCP is to make Freespace even more than it was originally, it's a rocky road, I'll admit, but that just means we need everyone pulling the cart, as it were.