I read through the explanations and a lot of it is either because regions just so happen to share similar environments or features (mountain ranges, deserts, railways) or they're jumping to conclusions about a few things such as:
1. Using the water's color to decide placement. Kanto's is dark while Johto is lighter meaning Johto must be close to Hoenn's tropical environment. You know, instead of it being the game artist just choosing what color of blue looked nice at the time.
2. The swimmer swimming to Kalos from Hoenn was a little joke. It's nothing to base a feature of a map around.
3. Saying Parfum Palace is proof Kalos and Unova have a relation (which isn't too farfetched...) and thus the Kalos war was with Unova (... which is). Going even further saying Reshiram & Zekrom burned the location between them. Admittedly its odd that there's a statue of Zekrom & Reshiram among other Unova things in the garden, but who's to say the king didn't go to other lands and was aspired from something there and added it as a decoration? And unless there was another war the war in Unova was a civil war between the twin brothers and their dragons, not with another region.
4. He mistakes Unova's Cave of Being being "connected" to Sinnoh as it being physically connected. I think what they meant is that the Cave of Being has same features as the Lake Guardian's caves, a theoretical or spiritual connection.
5. He connects the Unova and Kalos railways. Okay, while for the Kalos's railway we don't know how far it reaches, we do know how far the Unova one does. We even have a map:
It's a self-contained system, like New York's subway line.
6. Says Unova and Oblivia must be close by because Latios & Latias can be found in both locations... the Legendaries who can fly as fast as jet planes and are known to migrate far distances. Also confused why Kyurem is in ORAS, did they miss the Hoopa portal you needed to interact with to battle it? Has a point about the Regi trio (and there's a few others I could mention) though I can come up with a BS excuse or write it off an non-canon.
7. Often uses the Professors traveling to locations "quickly" as a reason the regions are close by. First, we're never told how long it takes the Professor to travel, for all we know it takes a day or two. Also the Pokemon world has planes, trains and other vehicles, they probably took one of them. Also they're famous researchers who probably connections, if they want to go somewhere fast they can probably arrange it without any problems. Finally we can use a Pokemon to fly us to a city/town across the region in mere seconds seconds (or if you want to be realistic I give it a few minutes), so why can't they for much farther travel?
8. Says the Royal Unova would be a boring ride if it didn't have Kalos locations to go to. Even though when we ride the Royal Unova we just sail between the Skyarrow Bridge and Marvelous Bridge which takes the whole day. The Royal Unova is very likely a sightseeing cruise ship which New York have a few of.
Also they say it's never going to be truly finished because each gen adds a new region so they'll just add them when they come out. That's not how maps work, you can't just plop an entire landmass when a new region appears and say it was just discovered (and before you bring up Johto being the left of Kanto, Kanto's map only showed the Kanto region they never said it was the map of the entire landmass. Also FRLG sorta fixed that by adding a few references to Johto). If you're going to have this be the conclusive map of the Pokemon world it sort of needs to have room for new regions on it.
Now the Pokemon world probably doesn't match 1:1 to our world, it would be ridiculously to think that it did. What I'm saying and what seems to be the case is that the general placement is probably what's intended.
Would be nice for GF to release a map showing where everything is, but as I said above that might risk them either having to add new landmasses for a new region making them no better than what this map would need to do or, if they included plenty of space, be limited by that map's open space. For GF it's better to keep things ambiguous, saying its roughly like our world yet not exactly, giving them the freedom to say for certain where a region is located but not having to follow its geography exactly.
And look, I give credit to the person who made this map. They put a lot of thought in it that if the regions did exist on one super continent this would be. But they don't.