MTrackAlign

Hi, just bought this thinking this would help to align my double tracked guitars.
It seems to do a great job, but on some parts with (slightly) longer notes (2 seconds), the volume can go up and down, like if I was playing with my volume pedal.
I tried playing with all the settings, also changing the initial volume of my DI tracks, but either it does not align, or it has this small volume thing.

I would like to somehow tell autoalign to only concentrate on transients, I totally see the potential of the tool here, but I'll have to be very careful listening to the produced result, and maybe exclude some 'tails',
but then I'll probably faster, in Reaper, using my good old manual stretch points.

I am sure there is a way to slighly improve this (on my side I mean), and welcome any suggestions, as this tool seems to be such a time saver!

Thanks.