I strongly disagree. Obviously there are always exceptional circumstances, but if something is really a best practice, that means "if you decide not to do it this way, you should have a good reason for that decision".

Now I would agree that people are too quick to call something a "best practice", when really it's just their personal preference (e.g. "always use semicolons in JS", or "never use semicolons in JS").

The coding style guide put out by your 12 member startup isn't "best practice" for everyone. It's just best practice for continuing to work there.

Whenever something deviates from best practices, I would think that that raises a red flag for justification of difference.

I would argue that a quorum of engineers would generally agree with whatever is justifiably deviating from best practices. If it makes sense to you because of good engineering reasons, then it should probably make sense to other engineers. Reality perhaps dictates otherwise, but that's what it should strive for.