I have not noticed any difference, even for the B.
the main reason i've heard for thru-body is from one person on the G&L boards who had his bridge separate from the body of an L-2500 that was bridge strung.
I think that was an isolated event; I've had no problem with my l-2500 that's bridge strung. (also have L-2500 that's thru body. both sound great, as they should
if you look at the screws securing the bridge, there are only a few on the 2.5 because the thru-body holes are used for screws on a 2k. stringing thru the body will eliminate any chance of the bridge lifting. (note that the bridge on a g&l also is set into a slot in the body).