Shopify - 404 handling issue. & Are sub-collections possible?

Anyone here experienced with Shopify SEO? I'm an experienced SEO, but new to Shopify as I have a new client using it, and I'm getting frustrated, quickly. I have 2 main gripes, if anyone can shed any light on?

1. 404 handling doesn't exist for anything you type after a collections folder. So for example, domain/collections/iron-on-embroidered-patches is a collection page of theirs. If you mistype that - great, you get a 404. But if you add anything on the end - e.g. domain/collections/iron-on-embroidered-patches/cool - you don't. You just get the content of the collection URL, but the non-existent URL gives a 200-OK. This problem arose after I fixed the ridiculously stupid issue of every product sitting within a collection folder by editing the liquid files (don't even get me started on that!) - but the side-effect of that is the folder structure is now different (albeit correct for SEO), so I have a load of their crap old URLs which don't actually exist anymore indexed, and staying indexed because these URLs are returning a 200-OK. E.g. domain/collections/all/badges. So I'm going to have to manually 301 about 400 URLs. It also means I can't detect 404s properly in a crawl, and I guess it also means any such new URL could get indexed too. Shopify support don't understand, or want to understand the issue, so I'm at my wits end.
2. It doesn't allow you to have sub-collections. So for example, domain/collections/apples/red. Not possible. Which makes managing a large ecommerce site impossible. I've heard there are apps which enable this, but I've not yet managed to find one that does. Collections Unlimited looked like it did, but it doesn't. I'm aware I can sort of do it by using tags, but that means limited control over page content and meta data.

I'm probably going to have to hire a Shopify dev to fix these glaring issues, but before I do, if anyone knows any way round these issues first, that would be an amazing help :)

Also, if anyone knows if Shopify Plus doesn't suffer from the same problems, please let me know.

Cheers!

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