Only with a MOD that adds custom engines is this going to have any effect on any thing. Game stock engines all have the exact same thrust values and L_Drag vaules. Most of the shipwrights use a stock engine when making out ship packages so 98% of the servers out there this will have no effect on. BTW stock capital ship engines do require cargo space to mount, more then any stock freighter has so that is not an issue either.
Those changes are exactly what I am trying to do in the Hunters MK II mod; what I HAVE DONE with the MOD. I was specifically after the ability to alter speed and other engine details and then let the players decide for themselves which worked best for them and what was more important to them.
And you must not have looked at it as all the engines have volume (so they take up cargo space) and use energy. While it is possible for a VHF to mount a BB engine they are not getting off the ground with it because they won’t have the space left to mount a power plant.