Let me make a guess as to what is going on from your manager's point of view. They are short staffed and probably not getting a tremendous amount of support to replace the missing staff members. Their managers are not lowering their workloads any. They think the best way to get the extra work done is just demand that people do it, without any thought on what effect this will have on their employees. Ask a question or complain and get yelled at. The writing you up for "insubordination" because you asked a reasonable question is a gut reaction and bad management.
But, it always amuses me when people complain that they are already working a 40 hour work week. Oh, the horrors. Maybe it's just the industries I come from, but no one works a 40 hour work week. 50 seems to be more the norm. Perhaps it's unusual in your industry and I just come from over-worked land, but 40 seems to be a minimum.
So, what will happen if you take up the issue with higher management? Your complaint would need to be that the Best Practices manual is not being followed. So, you complain and best case scenario is that they tell your managers to stop it. If they truly do not know that these things are being violated (and the company cares that they are being violated), then it's possible that things can change. They could provide a way for the work to be done within the best practices framework.
But, it is also possible that the higher level manager will laugh at you because HR wrote that stupid best practices manual and everyone ignores it.
It's also possible that they are well aware of the situation and your managers have been complaining to their managers about their workload because everyone is understaffed and overworked.
The very real risk you take in complaining is that your managers will get into trouble because of your complaint. A person who will write you up when you ask a question, will continue to take out their anger and frustration on you, even if their boss's are "protecting" you because you made the complaint. And, the high work load doesn't go away and they still haven't fully staffed the department.
This is unfair and bad management, but it's also my prediction of what would happen.
Now, please note, if these best practices are in anyway related to regulatory issues that could get your company in legal trouble, you must report it.
Inquire about plans to hire more staff. If the answer is that they are working on it and it should be soon, then super. Suffer through for a few more weeks. If the answer is that it will be a long time before they can hire someone new, then you have a decision to make. Are you willing to work in these conditions or not? It's clear that your complaints will be ignored and punished, so normal advice to stand up to them will result in your eventual termination. I don't recommend that course of action. Instead, you need to decide to leave and start pursuing a new career or decide to deal with it. The new normal is 5 open requisitions instead of 4 and 45 hours instead of 40. Exactly what you want? No. But, practical? Yes.
I'm sorry I can't give you magic words that will make your managers kind, friendly, and understanding. But, since the only person we can change is yourself, you get to do the adapting here.
Photo by EdinburghCityofPrint, Flickr cc 2.0