Separate balancing for instanced content definetly not happening, CRD's are not getting removed either, obviously.
The only sensible solution, as you have said, is the reward distrubution for different types of content, ideally more people taking part of something should yield better rewards per person than if all of them were to go do solo content.
Although you dont want to plummet the solo content rewards into the gutter since that's the main player growth source.
On the topic of "power creeping": I think in a good chunk of cases giving weapons and armour multiple uses rather than a single one greatly improves variability and viability of those gear items.
In my opinion every armour shoud provide 1-2 or in some rare cases 3 non-universal utility options or a single universal utility option like healing or flat resistance increases: Soldier Helmet is a good example of combining I-Frames and Mobility, yet cooldowns should be buffed slightly to be on-par with boot-slot gear, Mercenary Jacket is a good example of an item with a single defined universal utility option.
Every weapon E ideally needs to have 2-3 ways to be dealt with aswell, any combination of interrupts, purges and I-Frames is employabe, and most weapons already follow that philosophy.
But you definetly need to pay attention of not overdoing it: examples are bows having hard CC on a 5s cooldown Q despite being an RDPS role, or Black Hands having the ability to counter ~90%+ of defensives in the whole game just by pressing E, at the same time requiring no stack requirements and being instant-cast, to both of which my only question is "Why?".
Overall the topic of "Soft-counters" is quite broad, so I'd just leave it here for now.
Balancing so many weapons throughout so much content is hell. however, at some point is it a mmo game (aka playing with other players against other players since it is full loot) or is it a solo game? This should show the main focus and since the cd's update the actual balancing for groups instead of solo were more than minimal until recently (which are great changes for zergs and some of the 5's meta at minimum).
obviously, we can't ignore cd's existing and staying. i do know that.
Just feel that Retroman was pretty clear he aimed at rock-paper-scissor gameplay for HG and CD's are just 1v1 HG at the end of the day. so this applies there too. not all items should be to counter all (looking at you cleric cowl). And people need to bitch about that being an issue since they want the one build do it all.
So yeah, the specifics how to deal for everything can be really hard. and i don't mind some builds only being good at one thing and one thing only while others are more varied and so on. the moment there is more than 2-3 builds to partake on about same "success" rate at "equal" skill is what matters and shows it's mostly healthy.
So at the end it still comes down to the paper-scissors-rock forced playstyle that seem to be aimed at since HG got equipment swap locked way back (which removed lots of skill from the game and cost to prepare for some fights imo)