Two main problems... first of all the fitting of the 100mm rifled medium gun in a slightly offset centre position led to problems with cracking because recoil was not centred so were concentrated in places it should not have been.
To add a 45mm or 57mm gun would be much worse as these would be much more powerful guns with much more recoil.
the second problem of course is that the 40 rounds the BMP-3M carries of 100mm HE shells occupies most of the lower turret area so if you are keeping the 100mm gun there would be no room for 45mm rounds or 57mm rounds for that matter... 220 of which would actually take up more internal space than the 40 x 100mm rounds which are actually smaller.
In any case the 45mm and 57mm would be a good replacement for both the 30mm cannons and 100mm cannons. while they don't have the enormous rate of fire of the 30mm gun the guided shells means the kill probability is much higher with aimed single shots, and while each shot is not as powerful as a 100mm shell the high hit probability means fewer shots will result in more effective damage because you will be hitting what you are aiming for.