LET ME JUST PREFACE THIS: I always have a hard time exlaining exactly what my mind means!!! The numbers are easier to verbalize than to write.......
As far as the intonation and the variations of such on a marker changed by: a fingerboard plane, bridge adjustment/re-cut, post move etc. EVEN all of the above, the variation is far too inconsequential for the player needing the marker or any player for that matter.
WHY?
The repeatability of the human/hand is less exact than the change or movement of the dot marker.... example:
String Lenght of 42" D stop is at 14" SL/6 x2 then the octave is at 21" or 1/2 of the SL
SL of 42 1/2 D stop is at 14.05" thats a variation of 5 hunderdths of an inch or 1.27mm. and your octave at 21.06".
The above sounds to support the idea HOWEVER IF you change the height of your bridge ½ an inch from 42" (that’s quite a bit) and nothing else changes, your string length has ONLY changed roughly .07 of an inch. that’s 7 hundredths people!!! Apply that change to my equation for the D stop on the string lenght above taking a 42” length to 42.07 or the lesser 41.93 if the bridge was chopped down, divided the dif of both by 6 to find your D stop multiplying by 2 and you have a dif of .046 inch in the location of the proposed D marker. DO NOTE we are talking the extremes of the inch. Meaning taking the bridge from 5.5 to 6.5
Plain example: If you moved from the 42 to 42.07 via the 1/2 inch increase in your bridge height your D stop has moved from 14 inches to 14.02 inches…..CAN you even see that difference of .02" is the TRUE question????? Were talking .5mm if everything is kept strictly in place.
Yes this would make one "out of tune" if you were a computer.
A compounded change; sinking top, bridge cut, and fingerboard dress could however make these reference points bad. Even IF it were done on this "not so perfect candidate" the change measured above is less measurebale than the human playing the bass can make up for.

What the heck do I mean.....read again
That being said I am not a fan of inlays and truly a pencil user if needed, although I do gladly offer markers on basses when requested by the player
oh boy.....
feel free to check my figures