That is just goofy. I suppose they did that to add some distinction between products. What a PITA to have to manually run several programs or manually edit them just to add a T1, T2 etc.
One way to do it would be to save each file with the tool number specified: part1_T1.nc, part2_T2.nc. That would make it easier to manually edit them.
Here is another alternative:
http://www.cambam.co.uk/, download the free version and see how that works for you. From reading the Cut2D specs it look like they have similar features. The 'plus' version is the same price as Cut2D and has some enhanced 3D stuff. I have access to several big$ CAM programs through my employer but CamBam was the best 'hobbyist' priced product I could find (that did not do silly things like limit tool changes, or only do 2D or only do 3D.) to offer on my own website:
www.soigeneris.com.