I've had a few cars on a Q plate, it doesn't bother me at all, the car still drives the same!

There may be some impact on re-sale value, age related plate cars seem to be easier to sell. I think you might struggle to get an age related plate using a different engine.

Changing the engine post SVA seems to be a popular thing to do, particularly for a swap to a bike engine.

In the end I supose it depends on wether you want the hassle of doing the engine install twice.

Cheers

Chris