This rule was never addressed again, but there also wasn’t any need to:
this book gives level adjustments for the templated version of the creature
(emphasis mine)
By specifying “this book,” this sentence blocks itself from applying to anything found in any book but Savage Species, so there wasn’t really any need to update or change the rule for other books. (This has nothing to do with “primary sources,” it’s just what the rule says.)
Also, strict RAW, “templated version of the creature” would be an issue—that would suggest you need to see the LA on the sample creature write-up, and the LA on the template itself isn’t good enough. However, we can also see that they clearly didn’t do that—the sample incarnate construct stone golem doesn’t list an LA even though that’s literally the example they use of where they supposedly did this, and the only sample creature to have an explicit LA in the whole section is the tauric hobgoblin-griffon, which is a special case anyway—so that objection is only relevant if being extremely strict about RAW.
That said, the way they formatted playable and unplayable things did seem to change: it used to be that, for unplayable creatures, they just left LA out; that is, LA — was the default. You only saw LA — in templates that made something that might have otherwise been playable into something unplayable. They later changed it to make LA something they included on every creature (explicitly indicating LA — for unplayable creatures), and even though it was supposed to appear everywhere, they also stated that LA +0 was the default if no LA was listed (even though it was always supposed to be and that this is the opposite of what we saw previously). This is, obviously, a mess, and it’s my view that you can’t really claim stuff with no LA is playable; at best you can say it’s a mess and it being playable is one possibility among many. (You see arguing about this a lot around the unseelie fey template from Dragon Compendium, which has no printed LA of its own but has a sample gnome with LA +0 and is preposterously overpowered at that value.)