Hello lodewijk, I'm glad you are interested!
"Older units are phased out when building new buildings" means that units with a direct upgrade from the new building are no longer recruitable. I believe Dave Scarface did something similar in his original version, but it's been several weeks of modding edb's for me at this point so I honestly can't remember how he had it set up (I didn't keep a backup of his edb, unfortunately).
An example is the Saracen Militia. This unit is a direct upgrade and replacement for the Middle Eastern Spear Militia unit. Therefore when you construct the building that allows Saracen Militia, Spear Militia can no longer be recruited in that settlement. Another example is Mailed Knights. Once you can recruit Feudal Knights in a settlement, Mailed Knights disappear from the recruitment options (for that settlement).
I do not phase out units that may seem similar but have different gameplay functionality. So, for example, Archer Militia is not phased out once you can recruit crossbows, or gunpowder units... since archers, crossbows, and gunpowder units can all be used differently. Therefore, these units stay recruitable all through the game.
Siege equipment is handled a bit differently than the original mod. Ballistas (strong vs units) can be built all the way up until replaced by Mangonels (also strong vs units), instead of disappearing once you can build catapults/trebuchets (which are strong vs buildings). Essentially, I categorized each siege unit as anti-personnel, anti-building, or hybrid. Basilisks are good at everything (hybrid), therefore they are never removed, even when Serpentines (anti-personnel) become available.
I hope this makes it more clear than I made it in my OP.
Please let me know if you have any other questions, and if you try the submod I'd be glad to hear what you think.