Question: When it comes to using an LR parser generated by a tool, such as Bison, a disadvantage that often comes up as counterarguments is that the resulting parser will be unreadable and complicated to debug, which is true.

However, I don't really understand this argument since we just use one or two functions in the generated output, and that this last one is not supposed to contain any bugs (a priori).

This sounds to me like saying that we shouldn't use a compiler, because the generated assembler is not readable and difficult to certify as bug-free; but, I may not be aware of all the worries this could cause in a project needing a parser... so why should we care about this argument in the plan to use a a generated LR parser?

Answer: 
Enh... it isn’t a solid argument, but it isn’t something you should just ignore. Parsers are already a pain and a half to debug, so making them even more difficult to debug isn’t a great idea.

There’s also the occasional desire to edit the parser with certain rules that can’t be easily defined in grammars - sometimes for academic reasons, sometimes for performance reasons, sometimes because someone thinks it is easier to do the check there rather than as a post-parsing step.

Mostly though, when I hear this argument it isn’t so much that the parsing code is ugly, but that the output tree is ugly. This isn’t unique to LR parsers of course, but generated parsers do tend towards outputting unwieldy (but technically correct) parse trees. Some see the work to massage that into a nice tree to be nearly as much work as parsing in the first place.

Again, not strong arguments but situations that can make the generator a worse option than it first appears.
Put differently, what are the odds of a bug in a custom-built parser versus in a generated parser and the library code that Bison includes in your system? The Bison library code has had literally millions of uses, for decades. The generated parser will be peculiar to your input grammar, but again, Bison's generator has been used for 35 years.