To be completely honest, this sounds like a classic case of conflating hardware revision and configuration as it pertains to a managed configuration item. That you didn't have access to approved internal schematics, and technical knowledge of the black box was constrained to a defined external interface boundary prior to independent reverse engineering efforts is certainly consistent with that.
Class II ECPs consistent with MIL-HDBK-61/SAE EIA-649-1 and the system's documented objective maintenance plan are a thing. Surely the SMR code of this controller (more specifically, its maintenance repair and recoverability disposition indices as specified by AR 700-82 [1] that logistics activity would have assigned it) in the context of reported anecdote would be sufficient to infer an interesting story.
I certainly don't doubt that you encountered 4 different harware revisions, but it strikes me as much more likely that the maintenance plan for said system never intended internal hardware abstraction layers to be serviced by activity at your level, instead structured to be independently managed by contract activity driven by performance-based logistics incentives with the objective of ensuring that, from a black box behavioral perspective, what they reindoctrinated back into the supply system is tested to be operationally indistinguishable ("form, fit, function" as it were) and thus compliant with overarching performance specifications when integrated at the next higher assembly level.
[1] https://armypubs.army.mil/epubs/DR_pubs/DR_a/ARN30303-AR_700...
On the other side of the coin, I was one of those contractors in Afghanistan (2011-2013). I specifically co-developed an in-depth intensive five day course for all designated terminal operators. We didn't care what your background or experience was, we took everything from truck drivers to satcom techs through the same course. Taught the basics of RF theory, signal flow, troubleshooting, fault isolation, operations, and maintenance. Only the first two days were PowerPoint heavy(with very few words on the slides, mostly picture to relate concepts). After that, it was three days of hands on doing setup, tear down, and fault isolation. We would break all kinds of things, and they would repair it. All the problems we presented to them were real life issues that had been observed in the field.
The high point of that work was when one of the satcom techs came up to me after the course and said that they had learned more from me in a week than in six months at the schoolhouse.
As much support as we gave the folks we were there to help, it was all organic knowledge gained through experience. The satellite dish controller was a black box that we, as technicians had to reverse engineer because the company would not provide us with schematics. This was made worse by there being at least four hardware revisions (despite the company saying there were only two) with only some parts compatible across revisions.
The reason for not providing schematics? They feared one of us would clone it and sell it to the Army for cheaper, since it was the only custom piece of hardware in the entire system.