Not true. I just placed an order with two add-on items (totaling $7) and one non-add-on item ($20). The two add-on items were shipped separately.

Also, I'm pretty sure everything that's actually sitting in an Amazon warehouse is prime-eligible. The stuff that isn't is the stuff going through 3rd party sellers that don't use fulfillment by Amazon.

The intent is for add-ons to ship in a box with the main Prime order. This doesn't always happen due to the combination of what you order and the locations of the items across Amazon's fulfillment network. When this happens Amazon is eating the cost of those extra shipments and is considered a 'miss' by the inventory folks.

Everything in the warehouse is not prime. If fact, an item can flip from prime to not prime in near real time if the most accessible inventory is used up and all that is left is the stuff in the 'reserve' areas of the warehouse. This is the area where the giant boxes of inventory stored. Grabbing inventory from there involves pulling it down, opening, pulling apart eaches, and then stowing in fast access areas.

Before the concept of add-on items, anything shipped and sold by Amazon was eligible for prime. Add-on items are actually a limitation to prime, from a consumer/user standpoint.

Amazon has always had both Prime and non-Prime products in their inventory. Usually, 3rd party sellers are non-Prime, although some choose to use the Amazon Prime shipping system (and their products cost commensurately more). Also, products with thin profit margins, such as textbooks, quite often were and are not Prime.

Not exactly, there were items I buy regularly that used to be Prime eligible and were moved to add-on items. Amazon was borderline lying about that because they removed it from being Prime eligible for 1-2 days and then made it an Add On Item.