I find myself in similar situations, so rather than answering your question directly I find it easier to just share what I do :) Even as a dev I'm not completely comfortable with the Batch Tools, so I'm counting on someone saying "Oh man that's easy
to do, just use Batch Tools" but... Here's how I do it (lol)
There is a major set that I need to have optimized to the absolute maximum, and that's my "50,000 Base Damage High Mitigation Set with 6k+ TPS and 42k+ health fully buffed" set for Malygos and the like. When Ulduar comes, it'll be changed to
match the fights that are most tank-gear-dependant.
So I mark all my available items as completely regemmable and enchantable for that point. I then set my options, and optimize given the criteria of this most important role.
After they are all set, I go to "Current Items/Buffs" and ctrl-click the availability-diamonds for my equipped items from Green (any gemming) to Blue (only that gemming) and set the Enchants to specifically the ones chosen. They won't be changed
no matter what.
I then go ahead and change the options to "25,000 Base Damage High TPS >30k health unbuffed" which suits me fine for lower-naxx or 10 mans or heroics. Then I optimize that. It will use your current items that are specific, but regem any items
that aren't used in your Malygos set.
Though most of us working on these models would prefer for you to use our hard work; I find that if you keep your specialized set optimized, then just have your offset gear set to "general purpose" gemmings and enchants you'll wind up happy.
At that point you can just pick and choose your gear for those times where you just "need a bit more threat" or "need less damage reduction" through plain ol' common sense.
My favorite way of "eyeballing it" (even if it's not completely accurate because of the way upgrade lists work) would be to have the options panel open and look at your upgrade list chart in the comparison window. Fiddle with Boss Damage, Threat
Scale, etc and see at which points certain gear starts to appear on the upgrade list. For example the BV wrists from Naxx25 suddenly outperform the Dodge/Parry ones at around <20k base attack when it comes to Survival/Mitigation points.
Again, I'm 90% sure that there's a much faster and easier way to do what you want, but I'm generally happy with these steps; it helps me understand the gear relations a lot easier.
On a side note, Mana usage and regeneration (through Spiritual Attument and so on) being linked with Boss Incoming DPS is something Negarine and I were talking about implementing in the ProtPaladin model eventually, but it has been a rather low priority.