The first thing I noticed was that the Deep Mining research resulted in 50% of each and the <Iron ore/Copper ore/Coal/Stone> Deep Mining resulted in 80% of the specific one and 10% of the rest.
My line of thought was: "well, 80 + 10x3 equals 110, while the other sums to 200, which means that the specific one trades raw number to allowing you to be space-efficient in relation to the one you want, you'll have less resources, overall, but will use fewer constructions/space to get the amount you want for the specific one"

But, it turns out that the Deep Mining craft time is 4, and the <Specific resource> Deep mining is 7.1... I made a spreadsheet and found out that even for the Specific Resource, the <Specific resource> Deep mining is slower, and I actually tested in-game. I've put 5 Deep Mine, each with each recipe, and let it run for some time (with separate chests), something like 10/15 minutes.
When I came back, the basic one had about 200~220 of each (one machine summing 835) and the specific ones had 190~200 of the specific one, and 20~30 of the rest (each machine summing about 260~280).

That's working as intended to balance infinite ore generation of specific ores.

Basic deep mining produces roughly 1/4 the amount per ore of a mining drill before repeatable productivity.
Advanced Deep mining produces less additional ores and yields around 1/2 the ore compared to a mining drill.

It's not only the additional ores, it's also generating less of the specific ores, because even though the percentage is higher, the crafting time is even higher. So, as it stands now, the Basic Deep mining is better in every way.

Edit: just to mention, I'm playing Factorio 0.17.x (I think it's on 0.17.16), and using Deep Mine 0.4.3

Basic mining yields less than 10% more than advanced and has the drawback of large quantities of byproducts.

If anything advanced mining becomes too good when used for Bobs Ores.

I thought it could be because of the byproducts, but I was intrigued because of the part about Advanced Deep Mining producing 1/2 of a mining drill and Basic Deep Mining producing 1/4. This part is actually talking about Deep Mine 1 (Basic Deep Mine) and Deep Mine 2 (Advanced Deep Mine)?

Anyway, thanks for the explanations!