Yes, IEC 61131 programming paradigm is very different from others. I think you will be more confortable programming in ST (Structured Text) for your first times, but please take time to learn also the others (Ladder to a desktop / embedded programmer seems an ugly language, but when you learn it and in what situations it shines you realize you were plenty wrong).
Nonetheless, I feel obliged to say that I never encountered "lots of library clashes" with Epec. Also they recommend, on the 3606 manual
, Codesys proficiency to use their products: perhaps you did something wrong in Codesys and it blowed up. If you post some screenshot (or your project), I might help you troubleshooting it.
The reason they use 2.3 on the 3606 is that its CPU does not run 3.5. More powerful CPUs like those of 5050, EC44, XS6C and the 6000 series run 3.5, but they are more expensive (some significantly). But, except the ugly UI, Codesys 2.3 works well and it is very robust (other than not being a resource hog like 3.5 IDE...).