After some research we found out that iMX6UL(L) MPU is the widest used family for embedded Linux. So we started looking for a nice module with this MPU and finally found MYC-Y6ULX CPU Module (MYIR Tech Limited). You can see: http://www.myirtech.com/list.asp?id=572.
This module is relatively inexpensive, easy to use (no connector, just soldered on PCB). The MPU itself has a lot of communication and also one Ethernet PHY (so you need only a connector with magnetics).
Size of the module is suitable for selected enclosure.
The pictures above show the complete enclosure. It has DIN Rail holder (removable) and positions for 12 LEDs. The material of this enclosure is of good quality and it can be relatively well machined (holes).
This module has one Ethernet (directly from MPU module) on the front side, non-isolated RS485 line, power supply 24V +- 10% and 2 auxiliary inputs (for contacts).
The module also has a 10 pin connector (flat cable) for expansion units (non-insulated RS485 and power supply). And it has extra 20 pin extension connector (also flat cable) for custom boards (USB line, 8x GPIO, power supply).