Performance-wise you could go ahead an put down the 3 sections, then broadcast DecoFlakes in one final sweep Assuming the 45 mint limit the LiquaTile should still be wet enough to adhere to the falling flakes. But appearance-wise there is a chance that there might be a noticeable difference between the first and last sections.
If you broadcast immediately after back rolling the epoxy, of course, is still quite wet, the falling flakes setle in with many sinking almost to grade level. As the epoxy cures later broadcast flakes will tend to rest more on the surface above grade.
The difference may be slight enough to not be discernible, but if you want to eliminate that possibility spread the flakes immediately after back rolling.
Either way take a few minutes beforehand to practice spreading the flakes, and toss smaller rather than larger hand fulls, you can always toss down more, but it's impossible to undo an area with too heavy of a broadcast.