Indeed, the current TR has messed the Variable changes that allow you to set the Signature key items per each pillar.
I've made a quick edit to the 2 maps, to insta-spawn the items in the middle of each room without checking for Signatures (so that you can grab them and continue the story).
Mod attached.
First, get this Mod fix. Then, go in the Guardian (Gerda) fight and use Negotiations 3 times (you will climb her until you reach her mouth, but you'll lack the needed items), then Run Away from the fight. This then allows you to go to the sideroom paths.
At the end of each path, you would normally need to submit the Signature items to gain an item per each of the 2 siderooms (to then use in-combat with her in Negotiation). It currently is bugged in the TR, but I "fixed" the maps to insta-give you the needed items in the middle of each room without having to Submit the Signatures (since you guaranteed have all 4 of them by this point in the story).
You take the 2 items (1 in each room), then return to the Guardian fight, then Negotiate 3 times (3rd time you choose one of the top 2 options to use one of the items), then again Negotiate 3 times (to use the other option for the other item), then you win and continue the story. Good luck