In the remainder of the information you provided, it appears there were a variety of reasons, and if not formal charges, then still reasons why, including strong resentments of the judge which tried him, as you mentioned...
Johnson provided no footnote for where he sourced his own brief info, unfortunately.
Perhaps removal of the Ave Maria to substitute "Praise be to God" in school prayers was what set the pitchforks after the schoolmaster in the first place, leaving that aspect remaining to be included as reason why he was executed, though not inclusive of why, and possibly not showing up in list of more formal charges, similar to how political resentments of a judge likely would not make it into court record. That does leave one wondering though, just how much of what the man was charged with was actually as true as some would make it out to be.
That also leaves Johnson's scholarship not completely failing him on that point perhaps, though less than inclusive enough which perhaps he could be faulted for, but if the school incident was truly part of the bigger picture (it was, wasn't it) then other writers who fail to mention that could be faulted in part for that one "failure", themselves.
Johnson did not there write that the execution was by the Spanish Inquisition per se, but was a "Spanish execution for heresy".
That also may come across as misleading to a casual reader, yet is still technically correct.
Even when limited to being conducted by local level secular authority shows that they viewed it as their own prerogative, and in that sense regardless of having less than fully "legal" standing to do so, was in the end result much as continuation in spirit of previous Inquisition.
They did, and they didn't, with the Inquisitors playing papal office off against various Spanish kings.
When Church authority would make complaint, the Inquisitors would often in reply include response along lines "but we are acting under authority of the king" while of course reminding that they were ridding the world and the church of heretics "dangerous" to both Church & State.
When Spanish kings would complain, the Inquisitors would use the same basic process but tell the king they were acting under authority of the Church, according to Llorente, whom I do not believe anyone has cause to doubt on this particular point.
The trouble was they (the Inquisitors) were right.
But only partially, technically correct, yet enough to get away with it, with political considerations looming in the background promising trouble had either King or Church put their foot down and made an end of the entire ordeal. [funny how that reminds me of someone in the here and now world, that guy plays both ends against the middle near constantly, whenever pressed/in a jam/caught with hand in cookie jar. perhaps he is a blood descendent, or simply one in spirit]
If Paul Johnson was present on this forum he could say that he was still right in what he said, in every word regardless of what you had to add (he could add comment that what you said "didn't matter" if he wanted to be a jerk about it) and be just as fully justified (if not more) by the very same tokens of "technically correct" or "right" in his words, as you rely upon to do that same --- minus -- the skipping over/denying but producing no basis for the denial of the applicability of information provided which is inconvenient to the perpetual contention that you are never wrong, etc.
Your post changes nothing I said. Everything I said was true and accurate.