1. Reporting: Reports can specify Emails in Design Studio, however they will show results for any send of the individual email and will not be constricted to the program they were sent from.
2. Asset re-use in Engagement Programs: When using an engagement program, an asset is scanned for its ID. If that asset has been previously sent to a record via any other send, the engagement program will skip that send for that record. This could become a problem when reusing email assets housed in design studio in different engagement programs.
3. My Tokens: my.tokens will not properly render as they are based on a program folder. The assets that reference them need to be in the folder as well. In my testing, assets in design studio do not have a frame of reference for mytokens. Emails will not populate mytokens if they are housed outside of the program that owns the tokens.
With all of this noted, our recommendation is to utilize detailed templates in design studio and continue to clone your engagement programs and alter them as necessary. Although this presents some busy work in the short term, it pays off dividends in the long term when it comes to reporting, the use of my.tokens, and guaranteeing that records are sent the assets you are specifying in your programs.