Without knowing the requirements, you'll never know if they had a good reason for custom screws. As such this comment is not constructive at best, and just standard "apple is bad cause no standards" drivel at worst.
Firewire, USB-C, Bluetooth, POSIX, etc... Apple doesn't do as much non-standard stuff as people on the Internet would have you think.
I suspect they had to design their own screws however because most of the tamper bits have a lot of torque designed in which makes the heads deeper so they couldn't use an off the shelf design or it would intrude further into the chassis of the device.
Apple replaced my 6s before xmas 23 months into AppleCare with a brand new one because there was a light patch on the screen. Cost me £0.
People who didn't have the skills and didn't know a repair shop they trust could still pay for AppleCare, but AppleCare should have to compete on value, not be the only option because Apple locked down the product.
I have replaced various things on Apple products over the years myself and have had no problems at all. It's not exactly prevention!
https://www.ifixit.com/Teardown/Mac+Pro+Late+2013+Teardown/2...
It may be that there were some non-standard screws used in assemblies that were not disassembled by iFixit, but to me it is more likely that Apple simply used standard Torx screws in custom lengths.
Using custom-length screws is not "esoteric" design. My employer uses custom-made custom-length screws in its products, albeit at a much lower volume and with a much longer production time than I assume Apple is dealing with.
When we're designing something we don't look at the T5 screws available on the market and design around those, we design the product to meet its requirements and if that means getting a 5.125mm T5 Torx screw custom made instead of the standard 5mm available on the market, that's what we get.
Because of the industry I work in, we also have very strict requirements for the type of materials used in our products. If we need a screw it probably needs to be made out of a specific metal that has specific properties like A-286 or similar. You have to be guaranteed that the screws weren't made out of whatever metal was on the dock that day, with a label slapped on them after the fact.
We have thermal characteristics we have to meet, but Apple has manufacturing reliability standards it has to meet.
There is a near-zero chance that, unless you have a guy IN China going to the factory every day inspecting stuff as it comes off the line, a pallet of 5.125mm T5 Torx screws is going to contain screws that are all exactly 5.125mm in length.
Like Apple, we contract out the manufacturing of the screws to regional machine shops.
I have only been involved in the manufacturing side of things for about five years, but one of my first lessons was not to rely on dealers and distributors for mission-critical applications. One order of components we received from a very large and well-known supply house was slightly out of spec and set us back several weeks of work because it took time to realize there was a problem, determine what the problem was, and deal with the distributor to fix the problem. Now for one-off jobs we rely on an in-house machine shop and for bulk orders we contract out to local manufacturers rather than relying on a supply chain that traverses multiple disinterested middlemen on its way back to Shenzhen.
That way when the 5.125mm screws we ordered come out to 5.13mm our guy can get in his car with a baggie of screws and his Mitutoyo and go to the shop and show them what's wrong.
For every problem my small 130-man organization has encountered with manufacturing in the US, Apple probably has dealt with similar problems on a scale that is unimaginably larger, and in my experience no amount of money can fix those problems quickly.
Building stuff in the US is harder and slower than just saying "screw it" and slapping a badge on something pumped out of a factory in China.
No amount of money, not even Apple Money, can fix that quickly. People fail to understand this, they think money can solve everything.
Quite literally, if you have a hundred trillion dollars in cash and an army of buyers ready to spend it you can't fix most lead time problems.