Folks (including me some years ago) are always afraid of gearboxes because they do seem very complex until you see how they work. In all honesty they are not that bad. If you have no use for the current box and overdrive, then you have little to lose in opening it for a look-see have you? Even if you open it and end up with a pile of bits you are unable to reassemble there are folks around who can! The only tricky bit is making up a suitable dummy shaft to allow you to drive out the layshaft without dropping all the rollers out. I made up a 'perfect' brass shaft and still dropped all the rollers!!!!!! As noted above, the spline type isn't a deal breaker on input or output shaft. The length of the input shaft is possibly a problem if you want to use that box and the Commer bellhousing. Do you have the alpine bellhousing?
If, like me, you can't easily use the 'new' box and overdrive you could dismantle it to remove the overdrive and output shaft then find someone to fit them to your Commer box....
Of course it would be wise to test the overdrive on your existing box before going to the trouble of fitting it to the Commer!