Exactly. The spec-ECU is a pain in Dorna's ... b/c they have to find a supplier, rigorously test the new system and its integrity (performance and code security). Then they have to figure out how to enforce the rules they have written. If the MSMA would agree to 24L and rev-limits, the spec-ECU would be dropped. The electronics would still differentiate the best factories from the also-rans, but the costs of competition would be drastically reduced. Competitors have a much better chance to build a 1000cc engine that revs to 15,000rpm and uses 24L of fuel. The MSMA would have more competitors to defeat.
From Honda's standpoint, they already compete in a series with 1000cc, 24L, and a rev limit. Why should they compete in MotoGP as well as WSBK? Why not return to the days of 500 unit homologations and badass, fully-titanium SBKs (RC45, R7 OW-O2)?
Honestly though, if Honda can't figure out why pure prototyping is important without institutionalized plutocracy (via the technical regulations), GP is already done for. Honda are essentially saying, "if Dorna can't guarantee that the rules will allow rich factories to win, we have no reason to participate". Like Povol, Honda seem to think that the size of their wallet pre-qualifies them for whatever accolades they desire.