I don't see where Mach3 automaticaly applies teh tool offset with M6. What it will do is if you do not include teh H# with a G43 then it will aply teh offset for teh current tool#
M6 T1
G43 H1
OR
M6 T1
G43
Turn on tool offsets on the offset page.
Then in MDI, do this: (Make sure tools 1-3 have different lengths)
M6 T1
M6 T2
M6 T3
If you watch the Z axis DRO, you'll see that the G43 offsets are changing with the tool change.