I'd take a look at The Muscle and Strength Pyramid by Eric Helms - pretty much teaches you everything you need to know about programming for both hypertrophy and strength training at all levels. It's a far better book than Practical Programming for Strength Training which is where a lot of the programs you mention come from
How does Wendler's routine make one stronger if it seems to violate scientific tenants of how one develops strength?
I am currently reading through Eric Helms's book The Muscle and Strength Pyramid: Training, and his recommended rep and set range for strength training does not abide by Wendler's beginner's strength programming. Helms writes that, to develop one's strength, one should perform "⅔–¾ of [one's] volume in the 1–6 rep range [and the] remaining volume in the 6–15 rep range at a 5–10 RPE" (47). Using the volume load calculation (setsxrepsxload) or the sheer number of sets for my current numbers, it looks as if Wendler's volume of real strength training is far below the porportion that Helms believes that I should be hitting. This is true even for the more intermediate 5/3/1 routine that Wendler reccomends after the beginner's progression.
Get this book https://www.amazon.com/Muscle-Strength-Pyramid-Training/dp/109091282X
There its outlined how can you make your own program.
You don't know what you're talking about. Read this and then get back to me https://www.amazon.com/Muscle-Strength-Pyramid-Training/dp/109091282X
If you want to learn how to design effective programs for yourself I’d recommend these books.
https://www.amazon.co.uk/Muscle-Strength-Pyramid-Training/dp/109091282X
https://www.amazon.co.uk/Scientific-Principles-Hypertrophy-Renaissance-Periodization/dp/B08WP9GK36
It is much cheaper and faster to just pick a real program that is tried and tested and follow that.