First thing to understand that 'perfect' intonation is not really possible when all frets are parallel to each other, as well as nut and saddle.
Current fret spacing calculations are a 'compromise' or averaging of frequencies, and the ideal scenario that creates the foundation for the 'possibility' of perfect intonation is a 'fanned fret' spacing in which the treble side of the fretboard is more like we know it now, but the bass side is angled with frets further apart, and moreso as you go from nut to saddle, in much the way a folding Japanese Geisha holds her fan when open...
Doing the fanned frets removes the need for compromise in spacing.
Having said the above, it is surprisingly that most average folks have a wide bandwidth of how tolerant their hearing is of poor intonation. It takes some musical training unless you are born with perfect pitch, as well as having an instrument that has been setup at both nut and saddle, as well as the truss rod, if it has a truss rod, in order to get very good intonation.
If you ear is not trained or your instrument was poorly made, you will not 'hear' he poor intonation, but a tuner will.
If this is the dilemma, I'd first ask, has the instrument had a 'setup'?
I did not have the hearing perception for intonation being off unless it was off by 20 cents or more, until I got a concert Flea. I played it exclusively for about 3 months and then picked up my other ukes that had no setup and it was simply AWFUL.
My ear had adjusted to the better intonation of the Flea, and I set about learning to, and perfecting the setup of those other ukes, by adjusting the nut and saddle until the intonation was as good as the concert Flea. Which was no more than +2 cents at the 2nd fret and 100% dead-on at frets 7 and 12.
So, how bad is too bad? Depends upon your own ear.
Also, Intonation varies with string tension, which is a factor of string density manifest as the string diameter to everyone who is not a scientist, but depending upon scale length, intonation can very quite a bit, especially dependant upon string materials, nylon, Nylgut, Fluorocarbon, wound strings, etc..
so there is no perfect answer that fits everyone, but for my ear, if the instrument is perfectly in tune on all open strings, and is more than about 4 cents sharp or flat, I can hear it and it annoys me enough that I cannot play that instrument, it's like fingernails on a chalkboard to me, and and cannot be turned off
So all of my instruments are either setup by me, setup by the shop or vendor, or came setup by the maker to a very good level of intonation accuracy.
Once you get used to better intonation, there is no going back, you cannot mask poor intonation once your ear is attuned better.
You can 'decide' not to care, but if you are still playing an instrument with poor intonation, there is always going to be this horror of sour tone that you cannot
un-hear ever again.
Proceed with caution, as there is no refund possible once you acquire this ability, which is both a blessing and a curse.