I have been informed that Mach3 can only handle 1 pulse per main spindle rotation. I understand that this may cause issues with screw cutting and make's multi start threads a no go area.

That is not true and you can do multi start threads ...if...if .....your lathe "system" is accurate.
As noted by Russ and Hood, accurate / consistant spindle rpm will help along with adequate power so there is no slow down of the spindle.
For a single thread you can tolerate some small spindle change but with multistart .....the error will just show up and you'll have pitch problems.

You will find info on multi threading in the Threading on the Lathe write up in Members Doc's. see page 13 &14.
What i did know is in the write up.
I was barely able to do a good two start thread and three just didn't work for me here.
You want to see inaccuracy just scribe test and measure.
The # thing didn't work if I remember correctly and if you look at the code on page 14 you'll see that I just shifted the start point.
Been a few years since i tested.

RICH