While the advanced generation does do quite well with the automatic restrictions, the basic ones do not follow any rules and I can make calcite in space but not with the advanced calcite generation. So yeah, no idea why they are disconected

When you say "basic", are you referring to the Reconstruction recipes? If so, you can only get those if you disable the "Only Basic Ores" setting. You're right - it makes sense to add restrictions to those, as well. I added the option to support restrictions after I added Advanced recipes, and apparently forgot to propagate it into older content. Will fix promptly.

edit Fixed in 1.3.3. I added Surface Restrictions to Ore Reconstruction recipes for ores that had them. Good catch.