TL;DR - I think stock comments can be useful as guidelines, but not when they end up looking like copy-paste-next!
So I read a lot of the content posted here, and noticed I was writing very similar comments over and over, so I've kept a personal file of snippets for a while. Here are the guidelines I try to follow when using that.
1. Respect the writer.
If you see an answer that looks to have a significant amount of effort and/or that is very personal in nature, please, take that into account. It feels very disrespectful to put that much into an answer and get an autocomment in return. To the answerer, it looks like a rubber-stamp rejection of an honest attempt at a good answer, and that it was totally ignored and treated the same as any ol' bad answer.
They put effort into their post; respect that by putting some effort into your comment.
2. Use stock comments as templates, and add details to be as helpful as possible.
If stock comments were good enough, we wouldn't need to comment on closed questions! But we do, because it's not always obvious to OP where their post went wrong or how to fix it. (And because it's a lot more welcoming to see someone is willing to talk to you about it.)
I posted a few of of my personal doc's comments here... and you can see I added some disclaimers, e.g., on the backing up comment:
(You're encouraged to edit the last sentence based on the particular answer - for instance, to highlight a particular aspect that you feel is on shaky ground, or to encourage the user to expand on some experience or reference that they hinted at in their answer.)
While a stock comment is helpful as a starting point, it doesn't tell the user what exactly is wrong with their post. Presumably, if your hand is hovering over "paste", there was something in the post that tipped you off -- what was it? If they didn't "back it up", what needs to be backed up? Be specific and constructive.
3. If you don't have the time or energy to customize your comment, consider leaving it for someone else to review.
One major reason for using autocomments is to save time when reviewing, but if boilerplate autocomments are making people feel unwelcome and discouraged from contributing.. I'm not sure that comes out to a net positive for the site in the end, unfortunately.
We have a pretty good amount of users who are active in community moderation, so if you're feeling burnt out or don't want to deal with writing Yet Another Comment for Yet Another Not-Backed-Up Answer, chances are good someone else will be around who can take care of it. Don't feel pressured to review everything if you don't have the time or energy or desire to do so!
My personal doc is mostly a bunch of variations of sentences and sentence fragments, and I frequently update or tweak it. For example, when I became a mod I spent a good amount of time on my first comment explaining to a user how to get their answer undeleted, and from then on I've composed my comments like:
[what caused the deletion] [what exactly was the problem] [how to undelete]
The first and last points are usually snippets (and after the feedback in this question I updated them!), but the middle part is the interesting bit that really depends on things like - were there already comments explaining the problem? was it just flat offensive, or can it be fixed? is there a relevant meta post? is the user new, or do they have a history (good or bad)?
That doc is really helpful to me when moderating, because I sometimes take a while to find just the right words, and it helps me remember good phrases to use. But no two posts are exactly the same, and the more specific we can be in our constructive criticism of a post, the better.