As a long-time user, I’m a bit surprised by your “conclusion” that NGG was the problem. Particularly as you removed it and the site “broke”. Disabling a plugin is almost impossible to be the cause of breaking a site — literally you took it away. If it breaks at that point, it usually means the plugin was propping up a bad theme or plugin elsewhere. I’m also surprised that a supposed WP professional would be doing anything on a live site which is a bit odd too as you say you migrated it, so presumably, you would have migrated it to a staging site.
If you disable NGG, and the site doesn’t work, NGG isn’t the problem. What is MORE likely the cause would be a customized theme or a low-use plugin, considering NGG itself has more than 800k+ installs on literally thousands of different systems and works just fine. You might try the standard “fix” which is a) test on a staging site rather than live; and b) disabling all other plugins, switching to the WP Twenty Twenty theme (or equivalent) to see if it works in that environment. However, if all you do is WP Migrate (which clearly does not move NGG, see below and says so in its own instructions that it doesn’t work for sites with NGG, as does NGG itself saying it doesn’t work with WP Migrate), of course you break individual pages — all galleries that do more than simply style pictures from the media library, i.e. all galleries that are actually galleries not just blocks with pretensions — will not “degrade” gracefully as once you remove the plugins, the codes on those pages don’t work anymore.
However, fyi, the “non-standard” use of locations for its files are not a flaw, it’s a feature. Most professional photographers, for example, do NOT want their photos all jumbled together in the Media Library. They want them separate and protected from other plugins messing around with them. I’ve tried dozens of popular galleries, and quite frankly, the mixing together of files works if you have 1000 pics or less, better at 200 or less. It doesn’t work when you go to scale and want to host 100K photos. I have about 20K in so far, well beyond the limits of other galleries, and it works well BECAUSE of the separate file structure. Some installations are well up to 1M photos for professional photographers, and it works awesome for them.
As for your “warning”, it’s childish and laughable. I doubt someone who doesn’t even know the basics will be much of a cautionary tale for an plugin that is the most popular gallery of all time. But sure, you started with a broken site, you didn’t bother to read that WP Migrate doesn’t migrate sites with NGG, you have no idea why they would use a different file structure, you broke a live site rather than testing stuff on a staging site, think that disabling it broke the already-broken site, call yourself a WP professional, but blame NGG for the errors and then tell them “they’ve been warned”. I suggest you switch over to hosted blogger sites, seems more your level.
P.