1. The old traits provide protection against a problem that modern bacteria no longer encounter. As such, when changes to the genome interfere with those old protections, no problem occurs and the old protections are lost to genomic bit rot. (If a colony of Tibetans moved into India, over the long term their high-altitude adaptations would deteriorate under a lack of pressure to maintain themselves.)

2. Alcohol resistance is so valuable that +1 alcohol resistance makes up for -3 traditional resistance. This is the sickle-cell anemia model.

There is no conservation law holding constant the total amount of "protection" your genome provides you. If bacteria are adapted to defend themselves against certain risks, and you add a risk of alcohol exposure without removing the other risks, what you'll get are bacteria that (1) resist all the old risks (like the old bacteria did), and (2) also resist alcohol exposure.