Mojang does not, and never will, support mods in the common usage of the term (mods based on Java code which directly modify the game however they like), and especially not for versions as ancient as 1.4, which more or less no longer exist for them (they still let you play them but that's about it; even major game-breaking bugs caused by launcher/version updates, like MCL-5387 (note the "Downgrading is not, was never, and will never be officially supported") and MCL-6280, only have work-arounds given for them, not permanent fixes; in some cases you even need to use or make a mod to fix them).
If you want to know what Mojang has in mind for the "mod" API, they have already implemented parts of it as commands, resource packs, json files, data packs (upcoming in 1.13) and add-ons (PE/Win10) - it certainly is not going involve using Java code to modify the game directly (which is illegal for most software). Naturally, such an API will only let you make certain changes to the game and traditional mods will still be created, but will be (and already are becoming) far less common (add custom recipes (in 1.13) and custom blocks and items (actual new blocks/items, not based on existing ones, which they will probably add in a future update) and you've got many mods which add them covered).
For example, Pixelmon was shut down? No problem, you don't even need mods to play Pokemon in Minecraft:
Also, my opinion on mods that significantly change the game or add many new features is that you may as well see them as a separate version; Tekkit Classic for 1.2.5 is not really 1.2.5 and updating it to 1.12 or 1.14 will likely result in major changes to how it works due to all the changes and additions to the base game since then so it is no longer really the same mod (in other words, there is not much point to updating such a mod to later versions).
The "Better Together" update only applies to Pocket, Windows 10, and some versions of Console Edition, which will all be simply named "Minecraft", while the PC edition will be now be renamed to "Minecraft: Java Edition". The compatibility part simply refers to the fact that PE, Win10, and CE will all be able to play together on the same servers since they will all be the same game (all based on the "Bedrock" engine), with any differences being platform-specific (e.g. native OS interfaces. It may be possible that certain features, like higher graphical settings, might not be available on one platform or the other but they all will have the same blocks, items, mobs, world generation, IDs, etc).