1. Most of the surfaces are smooth, which makes air bubbles more visible. Alignment issues when building can happen more easily, if this appears to be an issue, glue the pieces with a non-scrape side down. Painting will also be slightly different, again something you'll just have to experience. I reckon the boys will enjoy experimenting with such (unimportant) details, so just have fun with it.. try some things.

2. The starship wall mould would obviously be mandatory. The medical lab has some pieces you can find suprisingly interesting uses for, so it may spark their imagination in an entirely different way. The cargo bay mould has some bits you can use the entire time and it'll just look good. Plus it has the cargo.. so again, plenty of uses. So I'd recommend the starship wall mould with the med-lab and/or cargo-bay mould, and add the starship deck mould. That floor mould is definitly a must. With just these moulds, you can allready make A LOT of things.

3. Afraid I'm not much help in that department, I'm sure someone else will answer this one for you though.