Jokers are usually done as the tail end of a program, after you’ve been building up your strength, at that point your true max should be higher than your initial max and could very well be above your estimated max - fatigue masks fitness and so on, usually Jokers are done coming out of a deload week and/or with a 3/5/1 setup that has the “5” week being less intensive and work as a semi-deload. Even then, you have to be honest with yourself and see at the moment if it’s one of those days when you can push the weight, or not.
The specific program you’re referring to has four phases (from 1.1 to 1.4), each builds on the previous one and it’s specifically said to run them in order and don’t skip from one to another.
If you just test your 1RM now, pick 90% as your TM and jump straight into the 1.4 phase, yes, you won’t have much room for Jokers and the whole mesocycle will be kinda pointless.
To expand a bit: even with the TM increases from cycle to cycle, as you get stronger your TM might be getting lower in terms of % relative to your 1RM.
Example with numbers:
You test your 1RM and it’s 110kg
You pick 90% and set your TM at 100kg for your first cycle
At the third cycle, your TM is 108kg (you added 4kg on your TM at the end of each cycle)
You test your 1RM again and you do 125-130kg, which means that your TM has moved from being 90% in your first cycle, to being around 85% in the last cycle, even if you increased it from cycle to cycle.
This has happened to me last year when I managed to push Jokers singles at TM+25% (beltless) and TM+30% (belt) on deads, after doing a PR set @90% and getting 13 reps, which is a bit of an extreme case but gives the idea.
At the time I was getting 10-15 reps during PR sets every time and managed to beat the previous weeks at every workout. I was also coming out of a stall in that lift.