I think we decided that tubes are underground. The only reason that the Op2 developers put them "above ground" in a sense, is to allow the player to know where the tubes are. Simply put, in OP3, we would have an "underground, or tube" mode, that would turn the terrain to a wireframe, and possibly the buildings, or have a lower opacity with the buildings themselves (I'm unsure how that should work from a UI standpoint).
This makes the most sense, considering that tubes must be driven on top of (and a huge cargo truck isn't going to drive over any tube that is sticking out of the ground without doing major damage to it)
Another option (if you've played the Moon Project you should know what I'm talking about, they do this with the 'power range' which shows little lightning bolts on the map when you push F9) is to have a mode where it just draws lines on the map indicating where tubes are.
The other thing would be to have 'posts' or some other type of object sticking out of the ground where the tubes are (and just place them in such a way that units would be able to drive past / around these posts without hitting them).
Think of things like poles to indicate where snow removal equipment should not go (if you live in a region that gets heavy amounts of snow), or those markers that are used to indicate the position of natural gas, water, or telephone system lines (where I live, large yellow tubular poles are used to show where a natural gas line is buried, you've most likely seen the smaller flags / signs to indicate fiber optic and telephone lines).
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As for the pavement, if you are to use pavement it shouldn't be a prerequisite to building (nor should it make buildings fall apart if theyre not built on it).
If it does anything it should just be like a "super bulldozing" where units go even faster and structures build faster.