1. Is there a way to make a mode so the titan factory can make more than one titan?
You can spawn as many as you want with abilities, but you can't use the standard titan construction process.
2. Is there a way to allow all of the ability levels for the capital and titan ships like is possible for the star base?
No, other than compressing the levels (before Rebellion for example, capitalships abilities only had 3 levels for standard and 1 for ultimate, not 4/2, so a level 10 capitalship would have all levels of abilities unlocked).