Open rust usually means surface rust. Bubbles mean one of two things. Pin holes already in the metal, or someone used body filler to repair rust previously. Bubbles mean moister under the paint. It didn't get there through the paint. Most likely you will find when you remove the paint there will be small holes there.
Your only option to not have spots is to do the repair work to completion with paint etc. If you have a shop do the work they can blend the paint. Then you wont have to paint the entire truck. Or you can paint from the glass down, blending the A and B pillars.