They are technically based on third versions.
Glitch fixes in Japanese Blue have nothing to do with storyline, they are just technical updates, which were imported to FR/LG. Updating PC by Bill is just a small reference to R/S/E to somehow connect origins of Bill's and Lanette's systems. It doesn't really mean that FR/LG and R/S/E storyline are at the same time. And that "Bill's update" is technically just game design update introduced in FR/LG and transferred to Emerald.
HG/SS are actually more focusing on Crystal's storyline because of addition of Eusine following Suicune. Lugia/Ho-oh encounters are just added before League to make HG and SS slighty different and to make their mascots catchable before League. Lugia and Ho-oh don't have much impact on HG/SS storyline, actually no legendary has.
I can say the same about you. You disregards solid proofs and not only about games timeline but also about Kyurem being a mascot (which is already proven), possibility of R/S remakes and similarities between R/S/E and B/W.
And how could I not insult when you post false arguments, for example Aqua/Magma not being known by people. It's simply not true.
We can be making arguments forever and still nothing will be agreed, so let's just wait and see how thing will turn out to be. At this time we know that you were wrong about Kyurem being a mascot and it's relation to Zekrom and Reshiram. Imo you may be wrong about other things as well but it's not proven yet, so let's just don't talk about those things anymore.