I think any effect of the shape of the top if the fret would be minute. I think the issue to which you refer is one of "temperament". I know little on this, so here is a start via a quick internet search
Tuning The Guitar
Excerpt from RVA's link:
INTONATION
Intonating most electric guitars is so simple that every guitarist with access to an electronic tuner should be able to do it himself. And since intonation is also affected by one's individual playing style - how hard one presses down the strings, for example - it makes sense that a guitar should be intonated by the person who is going to play it.
The nut, truss rod and action height should be adjusted to taste before you start intonating, otherwise you may as well not bother. It is also a waste of time (except in an emergency situation) to try to intonate with worn strings. For best results, restring and adjust the instrument, and then wait 24 hours to let the strings settle before fine-adjusting the intonation. (By all means give it another check and final adjustment 24 hours after that, too.) For most guitars you will only need a new set of strings, a screwdriver or key of the correct size for the bridge saddles' length adjusting screws, a good electronic tuner, and patience. Don't attempt to adjust your intonation by ear (unless you have perfect pitch) you'll only drive yourself crazy!
The goal of intonation is to adjust the length of each string individually until it plays pure octaves between the open string and the twelfth fret, between the first fret and the 13th fret, the 2nd and the 14th, and so on, as closely as possible. Start by tuning all six strings with the tuner (and keep checking the overall tuning throughout the procedure). The guitar should be held in playing position - the tuning will be noticeably affected by gravity, among other things, if the guitar is laid on its back.
Using the tuner, first compare the open string note to the note at the twelfth fret. The tuner should give exactly the same reading. If not, and the twelfth fret note is flat compared to the open note, the string length is slightly "too long", and the bridge saddle must be moved towards the neck. Conversely, if the twelfth fret note is sharp to the open note, the string is "too short", and the saddle must be moved away from the neck. Adjust the saddle, retune the open string and compare again. Repeat the procedure until the two notes agree. Do the same for the remaining strings.
Adding length to the string at the bridge end to correct the intonation at the 12th fret has an unfortunate side-effect, in that this also lengthens the distance from the higher frets to the bridge, which can throw the intonation off at the top end of the range.
To check for this, compare the 5th fret with the 17th fret, and the 7th fret with the 19th fret. If there is a problem, it may be necessary to compromise the 12th fret a tad to get acceptable intonation in the high register. If the guitar is seldom played above the 10th fret, though, it's obviously better to optimise the low end instead.
All the strings will end up slightly longer than the theoretical scale length, which is the distance from the nut to the twelfth fret x 2. The thicker the string, the more its tension increases when fretted. The lower strings therefore need more "compensation", as this small increase in length is called. A plain string needs more compensation than a wound string of the same diameter, so, in most cases, the high E string will be shortest, the B string a little longer, a plain G a little longer still, the D string a little shorter than the G, the A string a little longer than the D, and the low E longest of all.
Heavy gauge strings need less overall compensation than lighter gauges. This is because they are already at a higher tension than lighter gauges, and thus the percentage of tension added by fretting the strings is relatively less than for lighter gauges.
