Why do games with gold not show on purchase history?

I believe its because itss through Games with Gold and you didnt purchase them through your account directly but you did such through a subscription. 

As other Ambassadors have pointed out, you don't "own" Xbox One Games With Gold titles. Those are yours to claim and use as long as you maintain an Xbox Live Gold or Game Pass Ultimate subscription. As soon as you stop subscribing to Gold, you lose access to those titles unless you buy them outright. Conversely, Xbox 360 Games With Gold titles are indeed yours to keep and are considered owned.

To answer your specific questions:

Why is this still an issue? Games with gold has been a program for years, but we have no record of what we get through it. Games pass is screwing up games we already own causing us to lose access to them, or masking them making us buy them again.

When you access a game, your console checks for the licensing used to run it. There are multiple forms of licensing, with the first being the most direct - you bought it digitally, so it's connected to your Microsoft account. It also looks to see if the particular game disc is in the console's drive. It also looks for subscriptions that you have (Xbox Live Gold, Game Pass, EA Access, etc.) to see if that subscription grants you access to the title. I have not seen a game that was on Game Pass that then subsequently was removed have problems if I already owned it (for example, I bought Onrush on sale before it left Game Pass, and it works fine).

All of the technological advancements Microsoft has made to the world and they can't show us an accurate history of purchases and games we already own?

That history exists in your purchase history in your Microsoft account. Also, as you browse the Microsoft Store, games you own (or that you can access through a subscription) are marked as "Installed", "Owned" or "Available through [subscription]".

Why is the option to purchase a game we already own (either via purchase, or via redemption methods) even there? Why does it not change to a gift purchase option like non games pass games do?

When you look at a game in the Store that you own outright, it changes the "Buy" option to "Install" (if it's not on the console you're signed into) or "Play" (if it is installed). If you have the game via subscription or Gold, it indicates as such, but gives you the option to buy outright if you so choose. Again, this is because you don't actually own it. It also retains the "Gift" option if you wish to buy the title as a gift for another user.
It's the 21st centruy, why do we have to request a refund, and then wonder if we're going to end up losing access to things we already owned to begin with?

If you're requesting a refund on a title you purchased, that would be the only content affected when a refund request is granted.

I hope this makes things a bit clearer.