Savage changed the exterior dimention specs on the Mark IIs and 93. The Boyds stocks are currently inletted for the newer "E" spec barreled actions. I'm not sure what the differences are, but I'm sure that somebody on rimfirecentral can reply promptly in great detail.
I recently installed a Savage Mark II FV, pre-A/T, barreled action in 17 HM2 into a Boyds Rimfire Targert Hunter stock and had to do a little fitting to get the action to drop into the stock. I don't think that it is necessary to glass bed your Mark II action into your new stock, unless it is loose and/or there are obvious gaps in the metal to wood fit. That said, glass bedding is seldom a bad thing, when done properly.