I agree that many of those .0001 and below are often "in-housed" by the Broker's Market Maker. I see this happen with UBSS and Etrade using Citadel with their Option Market Making firm was akin to what you would refer to IBKR's "Timber Hill" routing.
Citadel is what drove me to move all my money after the 2008 meltdown when Citadel bought all Etrade's debt for pennies on the dollar and received all order-flow. Etrade had a Market Maker we traders use to laugh at, "GVRC" who took forever to fill a small order. The orginal traders got ARCA and INET free, the rest of the trades had to pay ".005 per share" to use ARCA and INET. If you wanted to catch a moving stock with a decent execution, 90% of the time you used ARCA. GVRC was horrible, taking five minutes to fill orders over 10,000 shares. We all learned to trade in increments of 9999 shares because the Market Makers did not have to show orders on the Level 2 of 10,000 shares.
You have a stock like GERN moving from $1.3 to $1.9 and Goober Market Maker can't even get you shares at $1.3 to $1.68 and finally on the fall to $1.53 your order of 15000 shares is printed at $1.68 while the stock hits $1.53 on the down side. The stock moves up again and I use only ARCA, ARCA, ARCA as other Etraders are getting slaughtered by GVCR.
Trying to get a cancel from Goober Pyle Market Maker was horrible until Etrade was taken over by Citadel. The adage to love the devil you know instead of wishing for a new demon comes true. Options no longer got any price enhancement $2.2 to $3.2 if someone is stupid to put a Market Order was filled at at $3.20 while my Fidelity Active Trader account filled orders at $2.75, strange how that works?
With the volume of trades I still do, and the amount of tape I go through, much of those trades you are seeing are "In Housed" to avoid ECN fees and "Matched" between Brokers like Ameritrade who claim they are able to in-house a huge number of shares without heading out to Nasdaq. The Dark-Pools FinraAlternateDisplay prints. High Frequence traders in my opinion are using BATS and EDGX exchanges. Just my opinion after watching the Time and Sales, Level 2 and NYSE-ARCA book for years.
You have to find a way to calucate how those programs are moving those stocks if you are a LL2 trader. Document how often they change their bid x ask, the spreads are bigger now in my opinion. Those Algos adjust quickly when nobody is willing to put a order out there. For three months I have traded UNXL and like clock work if you wait just enough time, you can get your buy order filled while the program hits the sell order .13 cents apart.
Friday, I had a order to buy at $19.13 and a order to sell at $19.29 and those machines hit my bid and took out my sell order in minutes. I churned the stock towards the close at $19.25x19.34, 19.29x19.38 and $19.33x 19.43. I know it's not all computers keeping the spread $.07 to $.19 apart consistently.
Maybe it's all in my head and those HFTS are not making the spreads on stocks like TSLA, Zillow and other stocks bigger than they should be!