The only down side other than some damage is whoever riveted the label plates on the front, did it upside down lol.
Rivots could always be driled out and new rivots used after making label plate right side up.
Im kind of curious as to airflow and spatial relation issues within your case. Best case scenario would be a ITX board o the motherboard takes as little space as possible. BUT ITX boards unless used in a server application, generally are not high end performance. So if you going to be playing games etc, it will be interesting what your limitations are.
Online I have looked at all sorts of hardware mods. One such mod that I really liked was a guy who mounted a older AMD Laptop main board sandwiched between two aluminum plates with stand offs to keep the main board from shorting out and PASSIVE COOLING! No fans needed. Thermal compound was applied to the CPU and GPU tops and the flat aluminum was acting as a heatsink. So the case itself was a heatsink.
The most extreme mod I have ever done was taking an older IBM 5150 which was dead and gutting it and cutting and fabricating the inside to make it run with a Pentium 4 2GB, 80GB IDE hard drive, 1GB RAM with a mATX motherboard out of a free emachine I was given that was originally a Celeron 2Ghz with 128MB RAM. I even salvaged some of the old 5150 power supply so that the big rocker switch could be used still to turn it on. The massive 5.25" floppy drives I took a ban saw to the cast aluminum and gutted them mechanically. One of them I measured and mounted a laptop DVD-RW drive so that you can insert CD or DVD discs into the 5.25" floppy drive and it would run the discs. I ran out of room though when it came to the power supply. I measured and measured and tried to figure out how I was going to pull it all off. It came down to me taking the innards out of a old dell computers 300 watt power supply and mounting that inside where the original power supply was, some rewiring also to make use of the original 5150 power plug to be wired to the newer power supply. Then came the fun of the cards to be added. The card slots would not line up with the 5150 cards. Its not a 1 for 1 line up. So I left the 5150 bays in vs cutting the backside out of it and made my own extenders. The extenders brought the PS2, audio, Ethernet, and VGA to the original 5150 back panel. BUT to extend I needed to add extender cables meant for KVMs etc. So I had say a 3 ft extender for a VGA that I only needed 10 inches but had to coil up the rest. Inside its quite a crammed mess or trying to fit everything every which way. To extend the ethernet I wasnt able to find a female RJ45 that would mount to a slot plate. So I took an old 10mbps ethernet card. Cut the PCB so just part of the PCB was connected to the slot plate. I then had to locate and cut all traces for the 8 pins of the RJ 45 jack on the remaining board to make sure it wasnt going to short since I just ban sawed the PCB. Then I had to take a Cat5 cable and cut a 12 inch section off the male end of the RJ45 plugs into the integrated NIC on the eMachine motherboard and then I had to wire one by one the wires of the cat 5 cable to the correct female pins on the butchered NIC card. Lastly was I needed a soft start push button. So I added a black push button to the left most 5.25" floppy drive and wired the red LED of the floppy drive to the HDLED FPanel connection on the motherboard.
This project took me about 3 months picking away at it. Hitting a modification road block and giving time to think about the best solution to keeping the 5150 to look as original as possible and yet run a modern OS and applications, and I didnt want to cheat the challenge and just stuff a laptop inside of it which would have been WAY EASIER but not as much fun!
Will check out the pics you shared when i get home, unable to check them out from work. Your project is interesting to me. Looking forward tio checking it out and helping with any mod suggestions you may need etc.