In my opinion, the BECM boxed sets are much superior to the Rules Compendium. (Never liked the "I" boxed set - which was pretty much ignored by the RC anyway.) They have better art, better atmosphere, and there are a few random minor things that didn't make it into the RC. The only thing the RC has going for it is organization, with everything being in one book - you don't have to check which boxed set a particular monster or spell is in, and you don't have to remember to go to the Companion Set for the War Machine rules but the Master Set for the Siege Machine. But on the other hand, the progression of rules added from Basic Set through Master Set makes it clear just how important each rule was intended to be (with a lot of the Master Set rules honestly feeling like afterthoughts - they were running out of stuff to add after the Companion!) in a way that just sticking "optional" on top of the sidebar doesn't.The main query your work here is raising for me is: If someone's interested in this period of D&D gaming, are they better off with the original BECMI rules or the Rules Compendium? It's unclear to me whether some of the contradictions and discrepancies you're uncovering would make more contextual sense in the original BECMI, or if it requires a more nuanced understanding of the developmental history of the rules.
Maybe it's just nostalgia, but the Basic set's presentation of dungeon adventuring, followed by the Expert set's expansion of those concepts into wilderness adventuring, really emphasizes the themes of this version of D&D, which is lost in the RC which puts all those concepts together.
EDIT: really, though, "this period" of D&D gaming is a little misleading: the focus of the Basic D&D line changed quite a bit over the years. The BECM sets were aimed at each supporting a specific style of play, with adventures giving examples of those playstyles: Basic was dungeon crawls (the prototypical example being B4 - The Lost City; B2 - Keep on the Borderlands is often cited but really it was written for original D&D and retrofitted onto Basic D&D, which shows how compatible they were), Expert was sandbox wilderness exploration (X1 - The Isle of Dread), Companion was domain rulership and the clash of armies (CM1 - Test of the Warlords), and Master was, well, kind of confused. But after they'd all been out for a while, authors naturally started to blur the lines between the different playstyles, starting with "transitional adventures" which were explicitly supposed to introduce characters from one set to the concepts from another (B10 - Night's Dark Terror, a wilderness hexcrawl for Basic level characters; X10 - Red Arrow, Black Shield, a clash of armies for Expert level characters) and then introducing the Gazetteer products, which were very in-depth looks at the setting which has been sketched out only briefly in the earlier adventures, and which ended up with a very different focus than the earlier products. Starting with the Gazetteers there was a lot more concern with telling stories than with the structure of adventures (which is common to the AD&D 2E adventures and setting products too - and to the 90's in RPG's in general) so the Gazetteers had lots of suggested NPC's and challenges that didn't match up to what was covered in the individual BECM boxed sets. For example an adventure for starting characters might involve a wilderness journey with low-level threats - nothing wrong with that, except that now you can't just pick up the Basic Set and that adventure, it's assumed you know what's in the Expert Set too. Or it might involve solving a mystery at a noble's manor - again, a perfectly fine adventure seed for a low-level character, but details from the Companion set tended to leak into the setting of such adventures so even though they're for low-level characters they're not "pure" Basic Set adventures anymore. And at the same time, a lot of the details of the setting and adventures changed in miscellaneous ways to the extent that the Gazetteer era really feels quite different from the BECM era. And the RC was specifically sold to support the Gazetteers, which strongly assumed that you had all the rules and setting elements (monsters, treasures, concepts of outer planes and Immortals, details of the demihuman clans) from all the sets, and mixed and matched them freely.
So saying I prefer the BECM sets to the RC is really saying that, in hindsight, I prefer the BECM style of adventures and setting support to the Gazetteer style, which was pretty similar to the AD&D 2E style. The BECM style is more unique and evocative.