Engine alignment within the subframe and subframe alignment related to the main frame are two seperate issues.
It is possible that the engine is misaligned due to motor mount problems that may be related to the accident or not. Such misalignment can be the cause of a shudder when pulling away from a stop, but doesn't seem likely that it would cause additional road vibration.
The subframe to main frame alignment is related to the wheel alignment. I would need to see the alignment readings to see if this is likely a problem. It does sound like the subframe is no longer aligned to the main frame since the alignment holes do not line up. This may not be a problem though, depending on the alignment readings. Shifting the subframe is one method of curing an alignment pull sometimes. So yes, changing the subframe alignment would change the alignment.
As long as you have a concern, you should go back to the shop that did the work and ask them about your concerns.