I have always applied this very fine viscosity sand sealer before I stain all my projects. It goes on like water and dries instantly but does make the wood proud again, then I resand. I always use 220 grit paper to get that super finish, but always remove it with a tack cloth, or air gun.
This does make for a uniform finish.
After staining I wait about two hours in the fresh air and then do the finish coat. I always use the water poly because I dislike that yellow finish and in many jobs I use water on the floors in business's that don't want the long drying wait and the dust that collects.
I am really sold on water poly. Have you tried it? You need multiple coats, and with 20 minute drying it is very practicle to do.
Just some differences in work tactics.
Your "wood conditioner" is probably the right thing to use, but I have found that they are so alike one works as the other.