Can I use Shimano's Di2 e-tube project software to do a custom lock out of additional small sprockets while in the small chainring?
My mountain bike doesn't have Di2, so this answer is based on my road bike Di2 experience..


  1) Whether there are options like 44/33/22 in the crankset dropdown, and


The e-Tube project software will only list crankset options that are actually available in Di2 series hardware. What I mean by that is if you're using a road bike Di2 Front derailleur (Ultegra or Dura-Ace) but a 105-series cassette/chain ring, you won't be able to select that. 


  2) If there's aren't super close options, can I manually enter my chainrings?


Nope! Sorry :(


  3) If necessary, can I ask the software to lock out EXTRA small sprockets on the cassette when in the smallest chainring?


Nope! But you could set up synchro-shift to determine when it automatically shifts to the next gear (and thus prevents cross-chaining for you). Note that the rider could always switch off synchro-shift (change to different shift mode) OR change from big to small chain ring when in the smallest sprocket and cause cross chaining that way.

More info on synchro-shift: https://di2center.com/2019/02/16/synchro-shift-how-does-it-work/ and https://di2center.com/2019/04/05/how-to-customise-synchronized-shift-settings/