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Just a comment from enduser perspective.

( I already struggle hard to get my small wiring project organized. "cable management" )
Diving into "building Linux from source", and fighting drivers etc. seems to be completely unreal.
Most (or only some?) people already having a hard time with the hal configuration and getting basic UI functions to work.

How many thousand hours do I have to spend extra in sofware research and learning new things, in order to save 60 coins on a control card?

Considering the cost of mechanical components (e.g. for metal working machines), the FPGA card is the least financial problem.

I feel that leaves a very small target group beeing interested in a "race to the bottom" with FPGA card pricing. This target group is also looking into 3d printer firmware and hardware. (cheap, and for some things usable)

I have had this gravel sound. Starts by sounding like tick, tick gradually transitioning to gravel and going back to tick,tick and disappear.
Repeats itself after some minutes.
It may not be what causes it for you, but in my case it was a slight difference in the DC cycle time and linuxcnc cycle time.
One is running slightly faster than the other. Both nominally 1 millisec, Combined with some latency of the linuxcnc computer
ethercat will send and receive data not from the current servo cycle, but from the previous or the next cycle.
The gravel sound would appear with the transition over this mixed period to stabilize when the cycles are so much out of phase that they always receive data from the same servo cycle phase.

You can check with halscope of the actual position for example. When the gravel sound happens you will see that
the actual position isn't a smooth line anymore as is expected. Instead you will see that it stays on the same
position for a cycle, to maybe jump double distance another. This is worthwhile checking. 
Two curves in halscope, commanded position and actual position, with and without gravel sound would be interesting to see.