The first draft with maximum possible dimensions (155x76 mm or 6"x3").
The RTC optional will be DS12885 in SMD case or DS12887 with built-in battery.
The CPLD will probably have to be in an SMD enclosure (I need to a lot of pins).

I'm thinking about choosing the display: 3-digit LED 7-segment, or LCD 2x16 characters. In both cases, you need to cut a hole on the display.
The encoder knob will also be on top the housing.

The big square hole on the center of PCB is for new, bigger radiator for NICK.

Thank you for your comment. This is the design stage when the assumptions can still be improved.

The hole is a hole
Somewhere you will need to place a display with information about the current status of all functions:
- system clock frequency,
- EXDOS clock frequency,
- configuration of ROM banks.
You can also display the date and time.
That is why I am inclined towards a small LCD or OLED display with 2x16 characters (about 20x50 mm).
It would be above the card.

The encoder knob must also be accessible to the outside.
EnterMice occupies the back. Edge connector on the right.
The top of the housing is left.

EXDOS controller and Gotek maybe it would be fit, but there is also a problem with space for external access to the USB connector and another display (maybe the display could be shared ?).
Besides, if you put everything at once on one board, the costs will get very high.
I will stay with the external EXDOS controller.

About Rom banking, do you mean to take, for example, a 64kb bank from the FlashRom and make it visible on some zone of the 4Mb space? Or simply the position of the whole 512KB?

There is a scarcely used zone of 64Kb over the cartridge memory(08-0F) that is ideal for the first option.

I was also thinking about throwing the system EXOS ROM into Flash.
Instead of exchanging and wiring the chip on the motherboard.
A good idea ?

I think it is a very good idea if it is possible, in this case EXOS ROM can be changed easily.

I intend to use SST39SF040-70ns.

About overclocking.
Because a square hole will allow access to NICK's, I invented to add a temperature measurement.
You can also set the overheat security.
If the set temperature is exceeded, the frequency would return to the default 8 MHz (or less until it cools down).

Temperature sensor will be optional. Type of the display too (OLED or LCD, difference with backlight).
My NICK has blurred marks. The glue from the heat sink has washed them away.

By the way. Is it possible a faster CPU speed than 10 MHz ?
I still have 24 MHz available, which I can give to NICK (12 MHz for CPU).