The scientist were worried that they would not disperse well in the body or collect in the "target tissues"

This is the opposite. They wanted them to stay in the tissue and/or require minimal effort to get them into the desired location for transfection. What they DON'T want is for them to go into the circulatory system.

It's what makes the tech work well (several hundredfold better then without the magnets)

That's just this particular type of delivery system. There are other systems that work well also. However, its a pretty cool system for targeted delivery if used with other targeting systems (externally expressed ligands for cell specific targeting e.g.).

then are they applying magnetic fields at the same time to activate the "vaccine"

If they are in fact using magnetite nanoparticles, and they are using an external magnetic field (for which I have seen no evidence in any of the "I got the shot" videos) then what would happen is it would help the nanoparticles get into the muscle cells, and not go into the circulatory system (at least make it much less likely). If they were using this tech for that purpose, that would almost certainly be a great thing.