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I'm also designed a mesa clone for a Raspberry Pi, currently in the process of testing everything.
Except for the reversed Sserial Pinout it looks like I got everything right.
You can take a look at my schematic for reference: github.com/jstjst/stmbl-fpga-master/blob...tmbl-fpga-master.pdf
Be careful the SPI In Out labels in the 7c81 schematic are reversed compared to the ucf file. Luckily I could fix that in the ucf file.
I routed some signals under the fpga, I see no problem with it. But try to have no completely hidden tracks so you can fix them if you got some connections wrong. In my opinion one of the more important things is the placement of the decoupling caps.

There are some pitfalls with the whole (fpga) programming (especially when using the Ethernet host interface). But with some reading through the forum I got everything pieced together, including recompiling mesaflash and linuxcnc. So it is totally doable (for reference, this is my first deep dive into linuxcnc and mesa/hostmot2, only used the RPi GPIO interface before, didn't use/own a mesa card).

Big thanks to Peter for providing the schematics and all the information that is on the forum!

Have you had any time to give a Dell OptiPlex 7050 a rub yet?
It would nice to get some feedback and recomendations regarding eventual tweaking :0)
Kind regards/Stefan

Can you reproduce this in one of the included simulation configs?
If yes then please provide a minimal gcode example (ie one that can actually be run when loaded) along with a clear description of when you are stopping the program and tell us what linuxcnc version you are using.
If you cannot reproduce this in a sim config then please also attach your zipped config folder.

As it is I cannot reproduce this on either 2.9 nor on master.