But over a long enough time, the roof and heating systems get replaced more than once, so that becomes a factor as well. 

I checked what we charge for roofs, siding, and concrete, all were within $.50/sq-ft of the mid point("better") based on direct experience in our zip.

We discovered a leak in the roof that will significantly increase rehab cost, making my HM Loan monthly payment too high to proceed.

The first problem I found was leaks, both roof and plumbing.  

After I purchased and began work, she added a new roof, ad hoc.

In fact a property we bought several years ago systematically failed in two well documented deficiencies, the roof & heating systems on both buildings. 

My question is: if I were to have a property inspection done, consider major costs that may come up such a roof and whatnot, and the dollars still look good for cashflow, should I go for it or is the nature of this type of property and neighborhood too big of a risk to even consider?

All I know is new roof in 2009.

However when it comes to condos HOA takes care of these things:maintain all structures, such as patching damaged roofs and siding, for example.

If you need to repair the roof, you will want to have $6000 for that, but instead of it coming out of your pocket, you want it coming out of the money from the rental itself.