Tom's build is, in and of itself, a useful 'fill-in' for Freespace 2 Multiplay, it's allowed people to play whilst FSO was worked on, however, it is not, and was never intended to be, a complete replacement to be used in preference to FSO.
That is the problem, by keep pushing people towards Tom's build when people should be testing FSO, people are accidentally causing a stumbling block. 3.6.9. is not unplayable on Multiplay, or at least if it is then people should be posting problems in Mantis and talking to the SCP people, not simply switching builds and leaving someone else to deal with it, certainly enough people can log on and play to mean that if there is a problem, it's a localised one.
Tom's build is not a symbol of something rotten, but nor is the SCP not worth bothering with om Multiplay when you have Tom's build. You should be playing 3.6.9 for preference and ONLY using Tom's build if you are having problems with FSO that simply cannot be fixed over the boards or via Mantis.