1. NextGenPVE only manages damage, not looting of boxes, etc.
You can use another plugin for that, e.g. LootProtect. However, I am currently trying to get some traction with the current maintainer of DynamicPVP so that we can also automatically manage zones there.
Unclear how RaidableBases handles this, or if it does.
2. DynamicPVP by default uses a ruleset called "exclude" not "include". However, whatever ruleset is configured in DynamicPVP will be managed in NextGenPVE.
Just make sure that whatever ruleset is configured in DynamicPVP ("TruePVE Mapping") exists in NextGenPVE.
3. DynamicPVP manages its zones, and will remove and add them as needed. This is the extent of the interaction between the two plugins: managing that list of zones dynamically.
You should not need to be concerned with the zone ids as they will change on every reload, etc.
4. However the NextGenPVE "exclude" ruleset is configured, damage should be controlled for the zones DynamicPVP sets.
Set the "exclude" ruleset however you want to control damage in zones managed by DynamicPVP.
As I understand it, the general concept of DynamicPVP is to manage zones where a PVE plugin will make exceptions to its rules. Usually, this means assigning a different ruleset other than default to allow PVP in those zones. As far as both plugins are concerned, the rest of the map is PVE only. I don't see evidence of RaidableBases integrating with either plugin, but my copy may be old.
Finally, there has been a lot of work recently to manage the null reference exceptions especially around heli activity. This is not yet perfect but you should update to the latest version.