Recently I had an issue regarding a site that runs 2 stores, but shared the same ROOT category between the stores, but had seperate categories per store (categories are enabled at store level)

The problem is that the integrated search service ( Algolia ) woudl index all products to all sites. The issue is that you could then search products in one store from another. This is not wnated, as they do have seperate products.

The only reason they sahre a root catalog is that all products do actually belong to both stores, which facilitates the ability to swap between stores, and retain products in cart from each store. So in effect you can checkout in either store with another stores products.

Search, however shoudl not be cross-site

One of the most time consuming, and frustrating tasks (purely becuase it is so mundane) is for a developer is to export external system databases, and re-import them for debug work.

In magento land, you need to alter a lot of database config values to make the imported database run in your dev environment.

This article describes a snaphot tool I created to allow quick, easy import and export of external magento databases into my development environment.

The standard magento way to sync orders placed, to external systems, is to use the 'sales_order_place_after' event. (This is even a question in the magento certification exam)

I have a problem with this: latency at checkout!

Using this (presecibed) method to sync your orders, you can add at least 3+ seconds (and as long as xx seconds) to the checkout process. That is unwanted lag, and delay for your customers, just to se their success page display.