Any impact or concerns when allowing management of content types AFTER application of Nintex workflows and forms?

Drew,

Good questions and as you may suspect, there is no major impact.

1. What impact, if any does allowing management of content types have on the original content type?
   1. The thing to note is that you have to configure everything to work when creating your own content types.  When using out of the box content types, Nintex handles this for you which makes working with the forms and workflows easy. 
2. To ensure the workflow launches on only the desired form, I guess I would set a start condition based on the content type's GUID, correct?
   1. I think you are talking about the actual start form for the workflow and yes you can modify that without much consequences.  This does depends on which version of SharePoint you're on also.
3. When I begin to design a workflow or form for the new content type, will I be prompted to select the desired content type when there are multiple content types in a list? I assume so, but how/when does this occur?
   1. When you configure new content types they will show up as options to use inside the workflow form.
4. Is there any online documentation regarding this? I searched online help using 'content type' as a search string, but no title of any document appeared relevant.
   1. Unfortunately there isn't much on just this piece, but if you look at forms documentation, the documentation applies as you're technically interacting with the forms product, even if its tied specifically to a workflow task, etc. There are times when modifying content types to creating new ones is necessary due to requirements.  I would suggest testing this at every point so you know what your modifications do, but its no different from anything else.