Does this chassis support a mini-itx mobo?

No, the SUPERMICRO SuperChassis CSE-512L-200B supports a maximum motherboard size of 12" x 9.6" ATX.

The back plate shown in the pic looks incompatible with the motherboard I want, can it be removed/swapped out?

The back plate can be removed. But I would still recommend using a supermicro motherboard as sometimes the alignment of the holes for the motherboard might not align properly with all types of motherboards. Also this is a 1u rack so if you want a IO/Shield that will fit you need to contact the motherboard manufacture for a 1U shield if they offer one. Or leave it out entirely if your unconcerned with the appearance or having a hole there.

What rails are compatible with this case?

It's a 1/3rd depth case for one-shot use - why would you want to put it on rails to begin with? Rails alone would cost more than this case - if you want rails I'd look into a more robust case to begin with. Just face-mount it using the front-plate and these are so short you can face-mount more on the backside of the rack too.

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SuperMicro CSE-512L-200B User Manual

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SUPERMICRO SuperChassis CSE-512L-200B Black 1U Rackmount Server Case 200W

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14" Mini 1U chassis support for max. motherboard size - 12" x 9.6" ATX
2 x 3.5" fixed drive bay
SAS or enterprise SATA HDD only recommended
1U 200W Multi-output power supply with 20pin, YM-5201D
1 full-height & half-length expansion slot(s) (Riser Card Required)
1 x 10cm blower

Overview

Specs

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MAIN OVERVIEW FEATURES: Motherboard Supported: ATXNumber of Fans Installed: 1Number of Internal 3.5" Bays: 2Number of Total Expansion Bays: 2Number of Total Expansion Slots: 1Total Number of USB Ports: 2Number of Power Supplies Supported: 1Number of Power Supplies Installed: 1Power Supply Wattage: 200 WColor: BlackCompatible Rack Unit: 1UForm Factor: Rack-mountableHeight: 1.70" (43.18 mm)Width: 16.80" (426.72 mm)Depth: 14" (355.60 mm)Weight (Approximate): 4.99 kgPackage Contents: SuperChassis SC512L-200B Rackmount Enclosure1 x Front cable (16-pin to 16-pin)1 x US power cord 18 AWG1 x 200W 1U power supply1 x 100mm 4-pin PWM blower fan1 x I/O shield for X8 server MB (3rd LAN + 4xLAN)