I've experienced the same thing with Sheiko having too low of an average intensity. I wasn't aware of him saying to adjust weights - maybe that's why it didn't work so well, lol. My form was still shitty when running strictly Sheiko so that was also a factor. Nowadays, I don't adjust up because my set program represents the upper limit of my recovery abilities. I don't adjust intensity down for high intensity, only volume.
At the moment I've been using Smolov Base as my volume phase for beltless squat since my squat sucks so bad. I've been using it more for practice since I've had a major technique overhaul and the program allows me to learn a lot in a short amount of time (especially when technique is at borderline failure) - the gains were a secondary goal. Since Smolov isn't sustainable by itself, I've made an intensity phase using a 4-week modified Sheiko cycle to peak all three competition lifts (including belted squat). Definitely not something people normally do but I plan to ride on the gains as long as possible. If it stops I'll move on to the CMS-MS Prep Sheiko programs. The plus side on the high volume is it's easier to put on muscle with the high workload and just hold on to the strength as I cut the fat.
Here's the 10-week breakdown in no particular order:
2 weeks of moderate-high volume/moderate intensity
2 weeks of low volume/moderate intensity
3 weeks of ridiculously high volume/low-high intensity
3 weeks of low volume/high intensity (90+ %)
Ignoring the fact that I'm crazy for depending on Smolov for volume, the program actually looks balanced in terms of volume and intensity. That's the main takeaway when looking at the overall program.
I know concurrent training works for a lot of people and I do plan to experiment with that in the future as well.
In your case, I agree with FlatsFarmer that you will make some big gains when introducing more intensity into the program. As long as you time it right. If I can't time it right, I'd just do something linear like an Ed Coan program and work backwards with the given time frame. That's usually the fallback plan, lol.
Edit: On a final note, maybe that's the problem with RPEs - only adjusting intensity and not adjusting volume. That basically supports your statement that there is too much emphasis on work capacity. Really, volume and intensity are both important at specific times so maybe it is better to allow adjustment of both. It would not make sense to me to not hit at least 90% for my last heavy session if I'm going for a PR soon just because I feel shitty. I'd rather take 1-2 singles at 90% (even grinders) than 3-4 singles at 85-88% during an intensity phase if that's the last heavy session before a PR.
Edit 2: Come to think of it, I actually did turn the modified Sheiko cycle into a concurrent program. I added a heavier single for the first two weeks (+5% intensity over main work) to allow an easier transition to hitting openers on week 3. Didn't think about it until now.