I had a think about this overnight/this morning, and I figured out a variation of what I used to do that provides a way around this mess (most of the time), allowing people to use Soil Enhancement (and the others after it) while leaving Planetary Soil Enhancement "in reserve" until Ultra Terraformer is researched, but it's kinda micromanagy and not readily apparent.
The way tile upgrades work, some tiles will only be unlockable as higher techs are researched. Perfectly understandable and logical. What this also means is if one clicks on Planetary Soil Enhancement, X number of tiles will appear that can be upgraded while if Soil Enhancement is clicked X+Y titles will be highlighted (with Y possibly being 0).
The trick is to flick back and forth and only click on the Y tiles.
The reason this works is because the "Y" tiles will be the ones in the .3 level of advancement while the "X" tiles will be the ones in the .4/.35 level. If one never upgrades a .4/.35 tile on a planet, it can't be "wasted". Pure math tells us so.
Then when Terraforming Plant is unlocked, rinse and repeat. Click back and forth between Planetary Soil Upgrade and Terraforming Plant and only upgrade the "+Y" tiles (if there are any). Same for Habitat Improvement and Resequencing Station.
In essence, by not using PSU, one is able to figure out which are the .35 tiles (and potential .4 ones) and which aren't and plan accordingly.
There are a couple of downsides, however. Sometimes there isn't a difference between PSU and SE on a world, simply due to random chance (there are, say, three .35 tiles bu no .3 ones). Slightly annoying, but once higher level improvements are unlocked, still managable.
The worse problem is the adjacency game. Because one won't always know what tiles will unlock at future points, one might end up upgrading a tile in the "wrong" spot. Yes, it is often possible to "guess" what tiles will appear eventually. But it's a chancy thing.
Now, all of this still applies only to the power gamers that are THAT concerned with wringing every last ounce of potential out of their planets. But it still can be a consideration nonetheless.
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tl;dr: Yes it is possible not to upgrade .4 tiles if one never upgrades the .35 ones. If PSU is never ever used on a planet until UT is unlocked, it can be used as a marker of sorts to upgrade other non-potential UT tiles.
Still a bit of a pain though (especially when taking over conquered planets where the AI has used a PSU). 
That idea of a tooltip that can be hovered over a tile saying it's Land Percentage (when trying to upgrade it, perhaps?) is a great one, IMO, as it would lessen the need to "dance" between improvements to see what is "optimal" to upgrade.
