Yes this can be an issue. For some unknown reason the #2 freewheel seems to wear more quickly than the #1. We did have a problem with what EC call "late engagement" - a slight overswing of N2 above Nr on engagement - which caused us to replace I think 2 MGBs before their overhaul life, although in both cases the MGBs were close to end of life (2000 hrs IIRC).
EC has been working on an improved freewheel unit for some time now and it must be close to being available, if not available already. Of course it can only be fitted when the MGB is sent for overhaul.
A factor may be where you get your MGBs overhauled. If done by a third party they may or may not have a policy of replacing the freewheel units regardless of condition. Since Bristow has EC "power by the hour" all our MGBs are overhauled at the factory.
Anyway, if there is a hint of late engagement the MGB should be replaced. It is indicative of excessive freewheel wear and the next step might be freewheel slippage under load with corresponding over speed shutdown.
You may be aware that, if you start the second engine by going straight to "flight" the engagement is fairly harsh, whereas if you start by going to Idle, then move to Flight once it has stabilised at idle, the engagement is softer. However I suppose this might help to mask the signs of freewheel wear and thus not be a good thing!