Again, in order to fully lock to your resolution as a design point, you may still need to pre-process imagery in order to get the right projections and power-of-two resoutions.
First And Foremost (and it shouldn’t be too terribly difficult) Rip out the nearest neighbor on that legacy GeoPaint tool or get rid of GeoPaint (at least for VT generation) altogether and use a nice bilinear or even let the user choose a cubic convolution. Yes it takes longer but it looks better. And then even if you do not pre-process the imagery, at least it will look a whole lot better.
Then yes - all you users need to chime in and beg for a better VT generator that allows you to use your costly imagery to its full potential and lock your design to that in a user friendly fashion.