I use IB's unbundled commission structure and exchange rebates to significantly reduce my transaction costs. I have tried to use the inverted cost structure exchanges on Bats BYX and Boston both before and after the market structure changes. However, I found that the use of those exchanges only increased my costs. If 95% or more of the liquidity is in the form of non-displayed front running, you gain little by being first in line for execution when that liquidity is exhausted. Even before the front running, I was pretty good at positioning myself on the right exchanges before the crowd and gained little by being one of the few who were on Boston (BEX) and later BYX.
As a market maker, you are always adversely selected. It generally used to be mostly by a few cents even on illiquid securities. Sometimes you would get filled at multiple price levels when a single large order hits a or from a flurry of activity, but the price would usually bounce right back. Now, all front runners get their fill and the rubber band stretches tightly before you get taken out. These days, they assume that you have a large amount of non-displayed liquidity to go with that single lot that you might be displaying. When your one lot or otherwise small order is no longer displayed, the displayed spread might become huge as all the algos remove the remainder of the displayed liquidity instantly.
I understand your thinking and it appears sound... If you carry it through, I'd really like to know how you do. IBPY, Matlab, or a faster (longer development time) direct interface through the IB API, etc. would be more appropriate platform choices. As you stated, Quantopian is not geared for that type of trading. I was actually looking for methods to automate my market making as you are suggesting when I found Quantopian. As a result of the rampant front running, I've decided to explore alternative strategies on Quantopian before expending additional resources to compete in a game where the structure of the marketplace has become such a disadvantage. Even if I find that I wish to continue market making, I believe that I'll get a lot of relevant knowledge and experience here.