Chiming in with my experience. I originally platted using the speedrun guide on the .org site. I was able to easily pop most trophies using a save I had from the final quest. All difficulties popped when I finished the quest. Bought one more book and bomb recipe for those trophies. I still needed cards on that save so I was able to finish that out the usual way with random Gwent games. Most combat trophies popped with one more time of each required task except for Overkill and Master Marksman which I needed to do from scratch. Finishing the last two contracts I had popped The Professional.
Assuming you made carefully planned saves it wouldn't be too hard to play both versions simultaneously. In my case I'm just going to do a ng+ playthrough on easy to get the story and contract trophies I still need.