1. Perform autofocus
2. Use a semi-clear lens such as zinc selenide to cover both sensors.
3. Place a half-silvered, front-silvered mirror in front of the visible light lens
4. In an inversion of 3, have a flat plate mirror of germanium
1 would work - but only at the [scene] focal plane
2 won't work because you still have two sensors on separate optical axes.
3 & 4 would work.
There is also 5 - where manual focus of the thermal lens is used to converge the optical sensor axis mechanically at the desired distance
With relatively wide angle lenses, and being at the 'cheap' end of things, these are not going to be worthwhile commercially. The old rule that spending too much on fixing a 'cheap' system means any buyer could simply buy the more expensive system that works properly in the first place.
You would also still get the phantom images issue of looking through glass - where 'MSX' tries to show a tree through the window in thermal.
Bill