Hailong Battery cradle mounting, is it okay to file off a small stand-off?

I am mounting a Hailong battery (cradle) (H01) on the downtime of an aluminum frame bike. There are three bottle-holder-mount threaded holes with stand-offs (raised area). I can use the upper two to mount the cradle, but then the third one kind of pushes the lower part of the cradle and causes it to flex up just a bit. I could just go with that, but I was also thinking of just filing that flush. IS that a bad idea?

You could put rubber washers/spacers on the other two so it clears the one in the middle. But yeah if not you could always file it down, but better to not make changes if you don’t have too.

Another option: You could relieve the plastic in the cradle where it hits the rivnut. (Large diameter drill bit or dremel tool, etc.)

Fyi the raised area is the edge of the insert, if ground flush it might fall into the frame.

is it difficult to remove the insert?

Yes, without leaving a chunk rattling around in the frame anyway.
Making a recess for it in the battery mount will prob be easier.
Maybe, depending on your mount, you might be able to drill thru the whole thing, and get a third bolt in there.