When laying out a TARDIS console, the sheet provides three slots per station.
There seems to be some confusion in the text as to whether an entire set of systems like "Navigation" fits in a slot (in which case eighteen slots is overkill) or whether, say, "Helmic Regulator" takes up a slot all by itself (in which case there seem to be too few slots to put all the Navigation controls at one station).
Am I missing an alternative reading that makes more sense than either of those?
The understanding I got from it was that those major systems /must/ be on the console, which takes up some ten slots. You then end up with eight or so to put on the smaller bits if you like. Each console panel needs at least one thing on it, but none needs all three filled in. For example, I have a Computer System on a panel, and Matrix Access right beneath it. I don't have a Helmic Regulator on the console anywhere at all.
My party's TARDIS, for example, has manual flight control, normally part of Navigation, on a seperate console so the Time Agent can leave the dangerous flying-without-entering-the-vortex-so-you-can-chase-a-cab-down-tne-M25 to the cute alien girl with superhuman reflexes. Of course, you could always leave a slot empty, or fill it with a coffee machine.
"Is there a word for total screaming genius that sounds modest and a tiny bit sexy?"
To clarify, as previously pointed out, the major systems are exactly that, a group of controls including everything mentioned in the TTC under that heading as well as extra minor controls (buttons, readouts, levers, etc.) that aren't mentioned directly. So Navigation includes the Helmic Regulator, Manual Flight Controls, Homing Beacon Circuit and Demat Circuit all under that one heading without you having to write down any of these sub-systems. Said Navigation controls can take damage from console blowouts, reducing their effectiveness by -1 until they get to -7, at which point they stop working altogether.
Not placing certain controls can make using them more difficult (characters without the Vortex Trait cannot use them at all if they are subsumed as minor less refined part of the larger set). For example, without a proper Helmic Regulator, the Time Lord is left using a much less precise sub-system on the Nav panel, and the GM might reduce the number of settings accordingly (you've got three settings, 'normal,' 'fast' and 'whoa, Nellie!') or just say that there is only one setting. On the downside, you have less control, but on the upside, it's one less thing to worry about.
The extra spots fill a variety of purposes. The first is padding. If you are keen on keeping your Nav systems operational, and don't particularly care about Manual Flight Controls or Homing Beacon Circuits, you can use the extra two slots to place those there. Now, when you take a console hit on that panel, there is only a 2 in 6 chance your main Navigation controls will take a hit and the likelyhood is you'll simply lose one of those other sub-systems instead.
The second purpose, as DaProfessor pointed out, is to remove a subsystem to another panel so that it may be used by someone else, even someone without the Vortex ability, or so it avoids damage from hits to the navigation panel, leaving you with a backup system.
Finally, there are all sorts of 'tertiary systems' that you can fill out the other slots with, like tea dispensers, mood detectors, whatever. These provide padding, but more importantly, they provide personality. And that's what the whole system is designed for: to provide you ultimate flexibility in designing a TARDIS that fits your Time Lord.