Ditto on all of that, In case you missed it, I described my current process for 70’s disco/funk with inconsistent tempos. Question about mixing track using loops - #11 by androphonic
That being said, as you point out there are anomalies happening. Overall, gridding with Engine DJ has been no worse than other software. Except, Rekordbox offers the ability to reset the bar downbeat, the first beat of a measure, and grid from there. This helps for those odd cases where there are measures with less than four beats and you want to rejig the grid. You can do it in Engine DJ, but you have to set an anchor and change the BPM, often doubled, to get the next bar to fall where you want it.