Thanks for the report but I don't expect to make further releases for 1.1. Also support for modded pipes (beyond SE space pipes in space zones) isn't something I planned.
You can add the steam drill to the blacklist setting so it is not deconstructed at all.
Autodeconstruct now has full support in 2.0 for modded pipes with different connection categories. If any mod makes a similar system where a drill can only connect to a certain type of pipe, it will automatically select the correct pipe.
