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Hello,

the real problem here is the #__assets table. If there is anything tied to such table (ie menu, single item access etc etc), you run the risk to corrupt the table, resulting in your site being completely broken. I saw a couple of site with a broken assets table and you really  want to avoid that.

Merging sites is not for the faint of hearth and it's very error prone.

What I suggest is to create a test environment. In such environment you can install and try out new things. Once you're ready with the result, apply the same changes on the live site.

I mean a copy of your website. You take a backup, restore it in a test environment (locally, on another server, in a subfolder etc etc) and try out the new things.

Once you're done, you (manually) do the same things in the live one.

I know it's a bummer, but we have found out that this is the easiest and fastest way to do it

I know, it's a bummer. Sadly having a central table holding everything means that if there are any troubles in there, your whole site would be broken, since it holds references to extensions, menus, modules etc etc.

On top of that, it's not a "regular" table, but it's a nested tree table, so things are even more complicated.

I'd strongly suggest you to get practiced in doing it manually, since it's way more robust and less error prone.