You've got a few things going on here.If "there aren't comparable properties within the radius they're willing to search", then you've got a property that is unique and virtually no lender wants to lend on a unique property.The reason they're only using comparable sales is because the broker/lender is selling to Fannie Mae or Freddie Mac and that's all they'll buy. 

You can use "tagging" type features to help you organize things by property if you'd like.In the end, you do what works for you, but I think that a set of accounts for each property can be a bit overkill.

They featured an attractive street urchin shoe shine boy, "Ragged Dick", who decided to work hard, save his money, who pulled himself up by his bootstraps to become a highly successful businessman. 

I like the search features: https://www.biggerpockets.com/searchThere are a few self-contained guides that you can access here: https://www.biggerpockets.com/guides

Have not used maintenance feature.

Paul likes to chime in on what he has experienced, but I think he is pretty unique.

I'd love a feature on the BP calc to include a borrowed down payment or an option to add a second mortgage.

As you mentioned, only half the property would have qualified and we had a pretty unique opportunity in North Carolina that we couldn't really pass up.

Every market is unique. 

I could have done that too, but if you know Newburgh Hts you can appreciate that its a unique area and comparing a property there to one in Clark/Fulton or Old Brooklyn didn't seem like the best approach to me to price it.