ISO is for alphabets with many accented letters that need to be placed on keys that can be reasonably touch-typed. Like most European alphabets. So the Enter ends up being farther away.
This isn't really accurate. The right-hand side of the keyboard has an equal total number of keys in ANSI and ISO. The only difference in count is that one single extra key next to the left Shift, and let me tell you, some ISO layouts use it for totally marginal ****, like "not that we really need it, but hey, as long as it happens to be there we might as well stick something on it".
Historically, Americans made keyboards for Americans, and mostly engineers for engineers too. The ordinary American user was happy with the A-Z, and the technical user also used the []{}\| part or whatever was offered. Then European use of the right-edge keys was partly constrained by the established American use - because it was generally all made by the same companies.
I have nothing against ISO in languages with larger alphabets, but in many cases, it does seem a little weird. For instance, why does the standard ANSI keyboard have []\|{}<> all accesible on the default layer? It seems sort of wasteful, when you think about the fact that a very small portion of the population even needs those keys with the regularity that putting them on the first layer implies. Replacing those with the extra characters in extended alphabets seems like it would be a reasonable thing to do, and just move those to the AltGr level.
Like most other little bits, just a historical accident petrified into a standard. Some doofus at IBM decided to make German and French layouts in a specific way, other manufacturers followed until that became the dominant form in the market, then it was retroactively blessed with the ISO stamp to destroy any leftover room for innovation.
(Don't get me wrong: the French used AZERTY well before IBM did anything about that, and that's not what I'm talking about; the doofus move was defining the Enter shape differently from American, which was not part of any standard by then.)
For some smaller languages (or poorer countries) it wasn't even IBM, it was some dude at Microsoft deciding how to "support" them in Windows 3.1 and what he decided back then is now touted as "the standard" for those languages.
Then again, most of those extra characters aren't characters, precisely, but rather accented characters. Devoting a key to them seems a bit excessive, in that some layouts (western spanish, for instance) you simply type the accent you want, followed by the vowel that you want, and you're good to go. If it works for them, why doesn't it work in Europe? You have `, ', : all easily accesible (where : would be umlaut), and it seems like it would be much more flexible.
It depends on what you do.
If I'm Swedish, I don't normally need crap like Ẽ Ě Ê Ĕ Ę so I don't care if they're made complicated to type or even impossible. But Å Ä Ü - and only those three - are ordinary everyday bread-and-butter letters for me, equal in importance to A B C, and I don't want to be assed to type them in a complicated way just because the keyboard was designed by some dude from another country who didn't need them. It's perfectly natural - in Sweden - to replace three of the near-useless (to a non-programmer) squiggly keys like [ and ] with those.
Imagine if the computer industry was instead dominated by the Italians, who generally don't need no steenkin J K W X Y. Imagine if American users were expected to type J as alt+I, K as alt+C, and so on. How much would that slow things down? Then if the Italians had already been wasteful enough to dedicate entire keys to []{}\|, English-speakers would reasonably want to remap those to JKWhatever.
Now, if I'm French, I do need something like 16 unamerican letters so obviously I need to find a different solution than just sticking my letters on the squigglies - and the French did find such a solution, for better or worse. But for languages like Swedish, Finnish, German, Slovenian that just need 3-5 extra letters, the most logical solution is exactly this.
ISO 9995 is an attempt at a truly international layout, "flexible" in the way you suggest. It will fail precisely because it's just too much hassle for people who need only a couple of extra letters from their own language, and don't care for the other 300 letters that are all equally complicated with ISO 9995. It's only potentially and partially useful to (a) people who need no special letters except occasionally to spell a foreign name, and (b) people whose languages already demand that they use sequences for their characters, because they have too many.
But I guess not as easy to type. Or then you'd be using the same keyboard as the filthy americans, or the dirty brits, or the evil french, or whoever the flavor of the week to hate on is.
I think this national idiocy you're talking about played into the silly decisions about where to place characters like + * ? ; and so on. Sadly. I don't think it played into the different-Enters philosophy, or a priori into the call to generally redefine []{}|\ as something else.