Disclaimer: I am answering about USB-A and -B connectors, C are bit much more complicated.
USB standard does not include magnetic connectors. Therefore, those can't be formally called "USB cables".
How should you think about such "cable" is that it's USB-A-to proprietary and then proprietary-to-USB-B device. The "device" part is crucial here, because the magnetic connector imposes own problems, like current limitation, reliability of connection, exposed pins and wrong order of making contact.
There is a crucial part of USB spec that makes simple magnetic connector impossible. USB defines plugging as a process. The ground and voltage pins are supposed to make the contact first, only then the data pins can made contact. So the device can power up and begin negotiation as soon as data gets connected. That's why data pins in USB plugs are shorter, so as you put the plug in, they make contact last. If I were making a magnetic connector (which, makes all contacts simultaneous), I'd insert a chip that would delay connecting of data pins to replicate the required behaviour.
I believe that the compatibility tables are mostly "made-up". They don't guarantee that the cable will be incompatible with other devices, they merely guarantee that the cable will be compatible with listed devices. This is most likely because the magnetic connectors are bulkier than regular connectors. Compatibility table is merely a manufacturer securing themselves against you returning the cable because "it doesn't work with my device".
On the other hand, there are also devices that use the voltage negotiation over old USB plugs. Eg my Samsung S7 asks the voltage to be bumped to +9V and the bundled charger delivers. It could fry a Charger Doctor, if I'd try to use one. So, it's reasonable that manufacturers don't want you to use a cable that's limited to 5V (by the chip) on S7. Either the cable chip can be smart enough to detect such negotiation and disrupt it or it'll fry. Thankfully, USB-C has it covered.
Fast charging that used to be enabled by simple pull-up in micro connector now requires "improved smart chip" and does not work with half of the mobile phones.
I don't know anything about that, can you point me to the spec regarding micro plugs? AFAIK there is no spec for resistors in connectors (if we exclude OTG and USB-C). Resistors are in the charger and the device determines max current by those resistance + voltage drop. Having extra connector on the way (which is weak and with small contact surface) surely adds some voltage drop, so the most primitive implementations (high currents @5V) would certainly be very limited.
Bottom line: I believe that limits on fast charging are mostly due to physics of magnetic connector itself. The order-ensuring chip has to sense a device being connected, so it most likely monitors current, and that most likely add a bit of resistance on +5V too, further limiting current-carrying capacity.
Some regular cables and USB gadgets also prevent fast charging, so magnetic cables are no exceptional in this regard at all. I wouldn't put the blame on the chip, but rather on stretching USB to it's limits.
Best Answer
There is actually quite an interesting design question hiding in here. You won't find a single connector part that will do what you want as it isn't a standard use case that would warrant mass production (i.e. nobody would make it because they wouldn't sell many).
The simplest way would be to build a PCB containing two USB A male connectors mounted in such a way that they will be in the right place. I can think of three ways this might be possible.
The first thought would be to get some SMD male connectors and mount one on each side of a PCB so that you get two connectors out the same side. However this would require to find just the right connectors - you would need two different connectors, which are basically the mirror image of each other (as one would be mounted on the reverse of the PCB. It would also require the PCB to be close enough to the right thickness to space the connectors.
An easier option would be to design a small PCB with one SMD USB connector on it, and have the second USB connector on your main PCB. The smaller board would plug in as a daughter board using some other connector such that the two USB male connectors are mounted above each other.
A third option would be to make a PCB which has two SMD USB connectors like these ones mounted vertically as if they were through-hole parts. This should be possible as they have pins that stick out the middle, and metal edge tabs that could be soldered to pads on the PCB for support. You would need to design the board with the connectors at the right spacing to mate with the Pi, and then route the connections down through the PCB to a different connector which would allow the board to be connected to your main PCB vertically.