I think it is a CYA thing because the spacers (knurled press-fit fasteners) are held in via friction. Mazda is saying (I think) it is impossible to re install in the same way that the factory "intended" without replacing the PPF with the fasteners pre-installed. In reality it is feasible to reuse them and I think the preferred way to remove the PPF is to remove them. First time I did this I resisted taking them out despite reading in Dave Wheeler's book that you need to. Dave was right.
You just have to be careful with the re install...either press them in ahead of time or make sure they are engaged and tighten the bolts slowly to avoid them spinning.
In terms of handling I can't see it as an issue unless they are loose and there is a gap there. I think this is just one of those situations that practicality takes priority over theory.
It may be possible to do it without removing them as the manual says, but I could never figure it out on my car.
Hope that helps