Perlite does tend to rise in the soil, especially when you water heavily.
It depends how thick the layer of perlite on top is, and how your root development is going.
But generally a layer of perlite on the soil is a GOOD thing.
It reflects light, discourages bugs and mold, and keeps dirt from splashing when you water.
When I am growing my seedlings I water them by standing them in a tray and pouring water into the tray. It disturbs the soil and roots less, and I bet it would keep the perlite more in the same place instead of stratifying.