I'd need to know more about what is meant by different tax structures.

MAS 200 v4.4 can most definitely be upgraded to Sage 100 2017. If you mean merging 4.4 into 2017 then you can do that in a couple ways as well.

I am curious about merging. We currently have two servers, one for MAS200 and one for Sage 100 2017. It would be nice to consolidate. 

Unfortunately the only info I have is:

"we CAN NOT set up the MAS 200 into Sage 100 because our tax structure is set up different so we cannot bring them together and a second company."

Do you have any enhancements, third party add-ons?

I'm not sure, where would I find that at?

Look at the Installed Modules Listing (Library Master - Reports).

If you are talking about Sales Tax, it is true those are configured at a system level, but as long as you use different code names for the Tax Codes / Schedules, you should be OK.

Be sure to bring in an expert.  There are some critically important considerations for merging data into a different system.