Tom the issues you discuss are well known
My point is simply always have a good backup outside your hard drive and don't rely on the so called backup that FTM makes.
Bare in mind that compact does more than compact the file. More importantly it re indexes all the internal pointers.
This is in fact a greater benefit than the actual file size reduction due to compacting.
So long as you have a goo back up and that you regularly test it by doing a restore to see that it works. Then I would not worry too much more about what FTM thinks that it is doing.