The MKL board is, of course, an auto-config device. Reason for not being an ideal solution for the A2000 is ... well, the auto-config chain.
Auto-config devices need a config-in signal and provide a config-out signal. When config-in is triggered, the ac-device activates its configuration registers so the CPU can read from and write to them. When configuring the device is done, the CPU triggers a signal that tells the device to disable its registers. When device is done doing this, it activates its config-out pin. Then the next auto-config-device gets a config-in signal. Electrically, this is done by using a device's config-out as the config-in of the next device in the chain. Hence "chain".
Note that "config-in" or "config-out" are not bus signals, but separate physical electrical pins in slots and on connectors.
Big box Amigas have several slots. Each slot's config-out pin is hard-wired to the next slot's config-in pin. In other words: The slots form a chain. (And there some logic involved to skip empty slots, but that's irrelevant here and now).
The MKL devices (v58, v59 and what not) vary in providing either only config-in, only config-out or both as physical connector pins. However, those pins need to be electrically inserted into the auto-config chain. Just plugging it into the CPU socket does not do that.
For example: Some MKL versions lack a config-in pin and, instead, logically assume their config-in triggered upon booting, so that the card's config registers are automatically visible. Unfortunately, so does the first slot in the Amiga, resulting in two devices occupying the auto-config memory space at the same time. Needless to say, that does not work.
If the MKL board in question only has a config-out pin, this pin needs to be connected to the next device's config-in pin, ie it needs to be wired the corresponding slot's config-in pin. That's a problem because
a) as mentioned, he first slot in order has its config-in hardwired as "triggered" (iow: you'd need to cut a trace on the motherboard),
b) the MKL board's config out never reaches config-in of any slot (iow: the board's config out needs to be connected to the first slot's config-in).
The "first" slot in the A2000 is the coprocessor slot. Its config-in is pin 12, which is hardwired to GND (which means it's active). Pin 11 is config-out. (Only on the A2000B, not the original A2000A)
See also page 94 of the A500/A2000 reference manual (for example
here)
PS: The same goes for A500s and A1000s with expansion cards connected to the 86pin side connector. Those connectors have a hardwired config-in pins for expansion cards. Therefore, connecting ac-devices with MKL-like boards sitting in the CPU socket requires a modification to the connector's config signals.