A lot of old houses that have been converted to apartments so you get weird configurations and have a lot more maintenance. 

I don't know why this new configuration is so tough on the eyes but it is..

For a variety of reasons if I were proceeding with this I'd try very hard to fit two two bedroom one bath units in there over the configuration you proposed.There's nothing wrong with your deal.

Conduct your own due diligence: Look into comparable properties in the area, even if they are not specifically 3:1 configurations.

It takes some tweaking and configuring and in the end it feels like I'm using it wrong. 

However, the Vendee program is configured so that the interest rate is 3.5% which makes for pretty good cash flow $300-400 a month however there's no equity capture.

My question is which configuration would be the best option as a rental?

But if you're changing the configuration at all and if removing your old cabinets will reveal flooring and wall repair.....forgit about it.

So with the configuration, you already lost $200 - $300 in rent a month, due mainly to the oversized furnace room.

., and then to justify numbers buy a house in a bad neighborhood, poor configuration, weird looking, sfr hacked into multi, small lot - no garage, un-permitted additions, etc etc.