The purpos of the delay between coats is to allow the previous coat to set up. Much the same manner as a painting process. If it is coated as a massive glob, then it will run off and puddle in the low places and the upper parts are just like they got one coat.
I prefer Extend Rust treater myself. It is chemically reactive to rust and forms a primer-like hard finish. Both work fine. To help with the seat tube water entry issue, make sure there is a drain hole on the bottom bracket shell. Doesnt have to be much, 1/8 will be fine. Then grease the neck of the seatpost collar area where the clamp splits, that is the primary entrance point.
Another steel maint trick that is always good is storing in a warm/living room temp at least periodically. The heat allows the moisture inside to dry a bit better.