It can be messy, especially if you're using enamels. Methyl ethyl kentones like Pro-Weld or Tenax 7R attack the paint AND melt the plastic.
It's inevitable that you'll have to repaint areas around seams and joints, regardless of what type of adhesive or welding agent you use.
Unless you're building a warship model, there's not much benefit in pre-spraying the major components of a model prior to assembly.
If you tell us what you're working on, maybe we can offer some assistance to make the process easier.
Regards,
Jeff