There is a huge variety of substrates that you can use for a planted tank, so everyone will look at their own and think it's the best and only way...
The extremes are probably from using an inert substrate like sand or gravel, which is cheap, long term stable, and doesn't contain or bind much nutrients, via different amendments in a lower layer, like laterite, peat, soil, soil conditioners or kitty litter, which can bind and release nutrients for plants, to a 100% Flourite/Onyx substrate, which maybe gets you the best results in exchange for a bigger part of your paycheck
And any and all combinations thereof.
But to answer your question. When you vacuum gravel (gravel vacuum, same thing?), depending on how thick the layer is, you will remove first any detritus/fishpoop, and if you go deeper you will suck out any finer layer if that's what you have below. If you use gravel over flourite it will get mixed up with each other.
When I vacuum I try not to clean to deep to not disturb the bottom layers, and my pea gravel layer is deep enough for that.
On the other hand, if you have a finer layer, like sand, over a coarse layer, like flourite, vacuuming this will over time bring up the coarser particles.
Keep in mind that even if you use something as sterile as gravel, you can supplement that with "root tabs" close to your root feeders for a slow release fertilizer supply. These root tabs can get really expensive though... so what you save first might get expensive over time.
If you use laterite or some other fine layer on the bottom, it might make your water hazy if you do a lot of re-planting. Roots just love that stuff, and don't want to let go when you pull them out.
Not sure if that answers your question...