Thank you again for your input!
I released an update that addresses some of your issues. Specifically: I updated the "PyEarlyMiniTrains" checkbox and its help text to actually be accurate: now it's called "extra early trains". If enabled, mini trains are available after logistics technology (as before), if disabled, mini trains are available after researching and producing py science pack 1.
I tried adding an extra fuel slot, but I think it's too easy. Mini locomotives are intended to be slightly worse than half of a regular locomotive, and if you use two mini locomotives, it feels appropriate that they would collectively have only two fuel slots, compared to a regular locomotive's three fuel slots. Trains dying and causing deadlocks should motivate you to upgrade to the next level of train, or to produce denser forms of fuel (eg coke instead of raw coal). That said, I added an "extra fuel slot" startup option that gives mini locomotives two fuel slots.