I'd say the question is, if you - personally - could deal with this situation
if everything else is perfect, and the engine exchange is documented as a factory warrenty swap, I'd say it's fine
but you have to deal with a "non-matching" car ...
a couple of years back, I used to own a 914-6 Sportomatic
it was high grade original, but the tranny was a warrenty exchange
luckily, this was documented at the maintainance record, showing the milage and the date as well as the dealer stamp
but, of course, the COA showed that it wasn't a matching numbers car no longer ...
so, you'll have to make your own mind about this situation