A customer brings in a bike with a loose bottom bracket, or they need a bottom bracket replaced. You have to take off the crank arms. You thread on the crank arm remover, but it isn't threading in smoothly. You see the crank arm threads are imperfect. What do you do?
Do you go ahead and just muscle the remove into the arm, damaging the already damaged threads, figuring you aren't hurting it anymore, and you'll be able to fix the bottom bracket, replace the cranks, and have a functioning bike?
Is it standard, common procedure to use a tool to chase the arm threads?
Do you refuse to work on it until the customer is made aware of the situation?

var and stein (and probably other fine tool makers) offer a crank extractor thread cutter. it cuts new threads for self extracting bolts. a good thing to have if you run a bike shop. (of course you'll have to stock the self extracting caps specific to the tool you have).
in any case, i'd call the client to let them know of the problem, since doing the extra work will mean extra money on the work order.

How can you cut threads when there's no material there? Or if existing threads are badly damaged?

The shop I work at has a couple of pullers with slightly larger thread than standard. Sometimes you can cut into what's left of the material with this larger thread and pull the damaged crank off that way. Failing that, a ball joint spreader and a big hammer can usually finesse the arm off.

I would inform the customer of the issue, and give them options of what could be done and what it is likely to cost. and as stated earlier a shop would ahve a the correct tool to chase the threads or repair with a self extractor.

do you have a good used crank to offer them?

Simple. By cutting oversize to m24 x 1.5. That's what the Stein and Var systems do.

Stein also makes an m24 x 1.5 shop crank puller, so you don't really have to get the self extractors.
I should add that the Stein system really does work well. No professional shop should be without one.

Inform the customer of what needs to be done first, then do it. Better to notify than to have to explain yourself after the fact.