In general is OK to seat a bullet .040 up the neck to compensate for a short case or a long throat chamber?
Depends. I routinely seat bullets at or just above the neck/shoulder joint with exceptional accuracy and to take full advantage of the powder capacity for velocity. If you are not using a heavy recoiling round/rifle combo and neck is sized for sufficient hold, you should be ok.
In more than a few of my BR and varmint rifles, either I partial neck size only or if it improved group size I use a neck collet sizer specific for the tension desired. In one BR rifle, a 1/3 neck size gave the best groups, so obviously little to zero tension on the remaining neck/bullet mattered little.
Uniformity seems to be the biggest factor, so unless heavy tension is required to maintain bullet seating during recoil or to insure uniform ignition of a powder charge before bullet movement, you can have very good results with minimum bullet seating depths.
So the answer is: It depends on several factors. Try it and see which is better for your situation.