Best to wait for Andy40 to respond as he has more practice and experience with DT than myself.

I found that 0000 steel wool just rolled the intensifier up into to tiny gummy sticky balls of crud and that light wet sanding with 1500 or 2000 did a better job without the dramas. And yes, I too experienced the flat shiny spots you are referring to.

For the intensifier over water based stain try a sample on a bit of scrap timber to see how it goes. Always best to experiment or practice on scrap timber just to be sure before attempting something different or that you are unsure about.