Most reloading data that uses .308 dia. bullets in the 54r do so for two reason some Mosin rifle mainly the Finnish rifles have .309 groove bores so they don't have to worry about overpressure issues from using larger dia. bullets. It basically a CYA thing.
A larger dia. bullet that is larger than the groove dia. of the bore will cause pressure to rise even more so as the charge weight increases. If your Vepr slugged out at .310" the .310" bullets will be just fine,velocity is going to be fairly high and the lighter 124 gr. bullet designed for the X39 will be very explosive,good for varmints and target shooting not good for larger game. You may even find that .308" dia. bullets will shoot very well or they may not,all you can do is give them a try and see,that would open up a whole lot of options if you want to develop hunting loads.
Anytime you change a component from the listed data you should start with the starting load and work up. An lastly you can always call the bullet/powder mfg. and talk to the ballistics guy about what you wanting to load up I've found them to be very helpful the few time I've had to contact them. Speer,Hornady an Hodgdon etc. etc. all have contact numbers on the web site.