As an SEO Geek I am (at least theoretically) with you. It would be nice to be able to add pages in the root.
However, from a SEO point of view the value is actually very limited and comes from the fact that:
Short URL’s a generally better - they are easier to share (more shares and links) and less often break up or fail (less broken links)
Only include relevant words in the URL
So with that in mind the fixed Shopify structure does have a slight negative impact. But it is, important to say, very, very little and you can compensate for this by:
Making sure the “handle” (the part of the URL you control) is short
Remove unnecessary stop words - keep only important keywords
The fixed part of the URLs (/pages/, /collections/ etc.) only take up very little space and add limited clutter.
If you follow my advice above and then do everything else you can to optimize your site then I promose you great SEO results on the Shopify platform. All platforms have some limitations or details I - as a SEO Geek would love to be different, but the fact is that for most of the much more important SEO-factors Shopify is actually better than most platforms (such as speed).
It seems that this is still not possible. My main issue with this is that my products have a QR code printed on them that takes users to mydomain.com/custom-url, so I need to have that page available on my domain. It seems to me that the only solution for this right now is to keep my Shopify store on a different subdomain and use a different content management system for pages on my main domain. Quite a pain to be honest.
In other platforms like WordPress you can toggle the publishing structure. It would be a HUGE win in the SEO department to be able to do this on Shopify. Posting here in hopes someone in the development team reads this, not necessarily to negate your comment. Anything you can do to remove nested URLs from your site is a boost for internal structure, which in turn is a boost for SEO overall. Internal site architecture is insanely important and not being able to control what the bucket is called, at the very minimum, is a big loss.