Carl, I don't see any reason to seat the bullets deeper over a "special" powder charge, seating normally will only decrease pressure/velocity a small amount depending on the powder you use. Of course, since the .41 Special is a wildcat and has been touted by several different people there are no SAAMI standards set for it concerning pressure levels and case length. Make sure you check the length of the cases used in the data you're looking at compared to the brass or seating depth you intend to use. If you're using a 1.155" length their won't be that much difference between the normal 1.29" lenth to really worry about. Trimming your brass to the 1.00" length sounds like a good idea to save on powder, but it's not. As you move away from the mouth of the case the wall gets thicker and seating a bullet too deep, or cutting it shorter will cause the bullet to bulge the case and may even prevent certain longer bullets from even being used. This was a problem with the .41 AE which was developed using cut down .41 magnum brass.
The best way to make .41 special type loads is to use powders that are generally found in other special cartridges. I use three basic powders, Bullseye, Unique and H110, for three different power levels in the .41 magnum, all using full length brass. I have experimented with the .41 magnum quite a bit over the years and found this to be much better than using shortened brass. Using a set of dies for the .41 AE I have tried various lengths of brass ranging from .866" to full length 1.29" magnum brass. And two that were even longer. The advantage of saving a little powder wasn't enough to offset the loss of accuracy.
One thing I have never understood was why Remington choose to use the 1.29" length to start with. Since there were no shorter and less powerful cartridges, and the weaker firearms that would have come with them, to worry about, they could have used a much more efficient case length. They were probably afraid consumers would think it wasn't as good as the other magnums if it didn't look like them.