you don't take the spreadsheet to the gym - it's just the method of programming. It's easy to be edgy and bash on well known programs that obviously work without any substance to back it up, 0ni pls go.
5/3/1 is designed to be a program that keeps on scaling upwards, and I personally have found the 'start too light' ethos to be sound advice. Obviously strength coaches might have their own opinions on what is more effective. I'd say that this sort of programming is aimed at people like me who train in commercial gyms or at home.
A beginner program generally has all of the main lifts 3x a week (due to light weight and ability to recover quickly from light weight) vs an intermediate to advanced routine where the main lifts (or specific body parts) are only being trained once a week, in this case with the user's own choice of assistance work depending on goals etc. Generally also in a beginner routine, you're aiming to put more weight on the bar with every workout, vs every week for an intermediate to every month for an advanced program.