Using one store and having self contained "stores" as collections

I’m trying to wrap my head around how to organize my Shopify site. I have a new company I’m creating that makes store fronts for organizations to sell merchandise that the main company produces. Over time this would hundreds of hundreds of stores and not be tenable as completely different shopify instances/accounts.

We were hoping to use collections as a way to create this basic structure all while having the ease of use of handling all the orders and transactions housed on one account.

So for instance an organization might have a designated url: sss.gives/nameoforg. This would direct them to a collection of products geared towards their org. Everywhere they would navigate would keep them within that collection so they weren’t accessing other organization’s collections. Each collection would use the same exact theme except maybe they have a different header image.

Is this possible on Shopify or is there another way to achieve this basic configuration?

Implementing the basic configuration you describe is possible on Shopify, but will require some customization work.

Using just a bit of code you can give access to collections to certain customers with certain tags, for example.