Is this the way to make good pies? I'm working in a small bakery shop and my boss is new to the business and have no passion in baking at all. He only learned it from his dad few years ago and his dad learned from other people too. 
I love baking but was told not to try anything different than what he's told me to do. 
At the moment, the pies I make, the flaky crust on top keep lifting up after baked and don't know why. 
Here is how i make the bottom crust pastry: 


7kg of all purpose flour
3.5kg of butter (forgot the brand name and the butter is ok to leave outside at room temperature)
2.1L of water
Mix it for about 7 mins roughly until it combine together and sometimes it's quite stretchy after 7mins of mixing (is this normal?)


Here is how i make the top flaky crust pastry


6kg of all purpose flour
1.5kg of pastry gems 
3L of water
Once it's all well mixed, add 2.2kg of pastry gem on top and mix it for 1 mins just to roughly combine.


So normally I would just mold all the bottom crust into the pie trays and leave it at room temperature then add the filling then cover it with flaky top pastry that usually keep in the fridge for about 1 or 2 hours. I also notice that the top pastry need to be refrigerated for at least 2 or 3 hours before use, otherwise it is hard to cover the pie tray. 

After I cover all the pies with flaky pastry top, brush with eggs then usually my boss leaving the tray at room temperature for about 10mins as he would turn the oven on after I have made all the pies. 

My question is, are these the right way to make good crust pies and why is the top flaky crust keep lifting up after baked?
My question is, are these the right way to make good crust pies


You're doing things at commercial scale and with commercial equipment and ingredients, so your method is going to be somewhat different right off the bat. As well, the owner's goal isn't necessarily to make the very best tasting crust that he can. Rather, his goal is to run a profitable business, and that means making a crust that's sufficiently appealing to customers that he can sell it, and to do so as cheaply and efficiently as possible.

There's not enough info here to know whether you're just using regular old salted butter or something that's more shelf-stable. A bakery probably goes through huge amounts of butter, so maybe it's delivered every few days, and it's not unreasonable for butter to be kept at cool room temperature for a few days, especially in large blocks that have relatively little surface area.

Home bakers generally use as little water as they can to make pastry crust, and they'd mix it as little as possible and let it rest in the refrigerator to hydrate. The goal is to get the dough to hold together while forming as little gluten as possible, so that the crust is tender and flaky. Your recipe definitely contains much more water and calls for much more mixing than home recipes. It may be that more gluten is helpful to make a dough that works reliably with the machines you use to form the bottom and top crusts. Home bakers generally wouldn't have access to "pastry gems," which I'd guess are preformed lumps of shortening that give the top crust the desired flakiness.

You really have to be the judge of whether the crust seems good to you: how does it taste? Is it tender and flaky? Also, is it good considering the owner's goals: do customers like it, does it work reliably, and can you make money selling your pies?


  and why is the top flaky crust keep lifting up after baked?


It's probably due to steam building up inside the pie, and possibly even within the crust itself. Do you dock (poke tiny holes in) the bottom crust before adding the filling? Do you cut one or more vents in the top crust before baking? If not, steam is very likely the culprit.