I think the main reason why they have to refund is because the way the new system will work.
If I got that correctly, the new shared storage will work like a collection in terms that you register an ichor over there and then upgrade it in this tab, meaning they have to give the materials back because the ichor in its physical improved form will no longer exist (probably only the lv 3 vaivoras that come from CM,unless they remove them,too,which is likely,because the required materials will be much lower).
About the compensation: I think the reason why they want the items to be marketable is because many people invested silver into buying them, and not everyone will be engaged into upgrading 4 or more vaivoras with these materials, so they will need to give the option to resell the materials, especially since some(or maybe all, I never engaged in vaivora/goddess set/demon set ichor transmutation so I don’t know the detailed materials and procedure of crafting them) of these items were also sold via Leticias Cubes, which caused a huge backlash on KTOS.
Since the KTOS community was very concerned about the value of these specific items, IMC will have to comply to these concerns and refund marketable transmutors.
About the ark: I doubt there will be a refund in Arch Stones here. You will probably need to dismantle the ark and craft it through the new storage crafting system to receive the discount of 1/5 of the price, so only blessed gems,sierra stones and mystic tome pages according to the upgrade level will be refunded directly.
Again,they will have to return these items as tradable because they already did so in the past when ark stage increase costs were reduced, and in the case of Arch Stones, nothing would stop people from dismantling their arks right before the patch to receive tradable items since you can transfer the enhancement to the dummy ark or a basic ark and still receive the compensation for the stage enhancement.
On the Lucifieri issue: Here, we don’t really know which costs are reduced. It could be that only the Tel Harsha valuable and silver costs will be reduced, it could also include Karaliene costs with Arch Stones involved (which would be the more important issue in crafting the set).
Once again, handing out untradable items (Tel Harsha items are untradable by default) is not an option because not everyone wants to build 3 or more Lucifieri sets, especially with the new system providing an easy “dismantle and reassemble with scrolls to transfer awakening, upgrade and transcendence” solution in case you want to play something completely different.
All in all IMC seems to be driven into a corner where they need to open the market to these items, especially because there is a severe shortage and high prices that limit access of new players to these items. What the game needs is new players who have access to resources, and IMC probably wants to free these resources from seasoned players rather than introducing new options that lower the value of these items by default.