Will Toyota perform TSB's on your FR-S even though the TSB is only issued for the BRZ
 

For example, this "12-140-12 : Popping Sound from Trunk / Rear Shelf Area" problem is happening on my FR-S but there seems to be an TSB only for the BRZ at the moment for this. So will Toyota fix this TSB or will they waive it off since there is no TSB for the FR-S on this specific problem?

It will all depend on your dealer. If there's a fault like rear deck noise and you take your car in under warranty they should look at fixing it if there's a fault.

I took mine in with for idle stability and Toyota read up on the Subaru TSB copy I took in and actioned it for me.

Incidentally if you have rear deck noise have you tried the 30s fix I wrote up here as the TSB didn't fix my issue but this did? http://www.ft86club.com/forums/showthread.php?t=42065

toyota has a tsb out for that now, just take it in and tell them whats happeneing

Your dealer sucks if they can't find the TSB fix for the FRS on this.

-alex