And some of the older homes have beautiful style and architecture.

To do it legally, you will likely need to pull permits including a minor/major alteration permit, and you may need separate permits for electrical, heating, and plumbing, plus you may need draftsman plans or architectural plans.  

I'm looking at a commercial property (small mill building for my architecture office) with an asking price of $135k, needing about $100k in rehab. 

I am fairly familiar with the process, graduated from UB Architecture and Planning.From what I have heard the City does not approve the conversions often or ever though these may have been references of trying to convert properties that may have never been 3s or 4s before, not ones that were once and now are not.However, I would not rely on this 100% obviously and if would all depend on the property and way that is/was recorded.

He has also introduced me to his design and architectural teams, and he's giving me access to his construction crews at a great price.

Would need some legal/architectural advice here.In regards to the zoning standards, Boston has one of the most non-sensible/obsolete zoning standards in the country.  

I graduated with my masters in architecture, no student loans and a solid chunk of $ in the bank.

Architecturally, it was for sure, once a very beautiful home on a great corner lot.

In my city there is a historic 70 unit apartment that’s famous for its design and mid century modern architectural style.

My background in architectural design definitely helped along the way, as I was able to spot thermal enclosure issues which I then pointed out to the inspector.