Well I emailed the store explaining the situation and arranged to bring it back in the other day, where their tech/manager had a look over it. I'm not completely convinced how much things were remedied, and I can't say I'm feeling much better about it. Here's my account of what happened - I apologise in advance if it seems a little long winded.
I showed him the bass and explained the issues I'd had with the fret buzz and pickup height, how I'd had to raise the saddles unusually high (I'd dropped them roughly back to 'normal' before I went to demonstrate the buzz) and been informed by you good folks that something was definitely up. Initially when I said the neck was 'almost straight' he told me that was wrong and that neck's should never be that straight. I pointed out that I was confident Rick's should in fact be almost straight based on the various sources I'd read (including the manual), he didn't appear to believe me/accept what I was saying but then checked the relief and declared that it seemed fine (pretty confusing, since it was almost straight, but I let it slide as perhaps it was just miscommunication between us and as long as he accepted the neck was ok as is.)
Regarding the pickup height, he told me that in fact those pickups were not intended to be adjusted, they were at a pre-set height using a foam back and that the centre screw was merely holding the pickup into the wood (he removed the bridge pickup to demonstrate), and that there was only a millimetre or two's movement at best. I found this a little strange as I've never heard of a pickup that couldn't be adjusted to suit the players preferred action/pickup balance etc. Is this true in any way shape or form? Did I misinterpret what he meant (although I'm not sure how else it could be taken)?
Back to the fret buzz: sure enough it's buzzing like crazy. He raised the D-string saddle slightly to of course, no avail. He then claimed that the string gauge seemed to be unusual - that the D seemed to belong to a light gauge set. I told him that as far as I'm aware, stock Rick strings are a custom gauge, with a 'light' A+D (I couldn't recall exactly off the top of my head). He asked if I'd mind if he tried swapping in a standard D string - I didn't really see what difference that would make but thought what the heck, can't do any harm and might as well let him cover all bases (no pun intended

). So he got a set of standard Elites and swapped the string - no effect, obviously, still buzzing like crazy. He then declared that it had to be the relief (even though apparently it was fine to start with?) and gave the truss rods a tweak. This seemed to cure it - no more buzz. He said would I like to take the bass away and see how I got on from there, I was cutting it a little fine to make it to work on time so I agreed.
Fast forward a couple of days before I could actually get the chance to look at the bass again and straight away I realize I'm glad he let me keep the full set of Elites - as of course I forgot to get the stock D string back so the original strings are now useless (facepalm). Anyway, the fret buzz is pretty much cured (bar a little when 'digging in') but the relief on the neck is now as you would expect it to be on any other bass i.e. when holding down the first and last fret there's a credit card sized gap at the 7th fret. Is this an acceptable cure? Or should the neck definitely be able to be set straighter than this?
Obviously, I now had to re-string the bass with the Elites, and after doing so I knew with the all truss rod/saddle/string adjustment my intonation would likely be out. Well, it was out all right, by a country mile! I had to shift all the saddles back considerably to get it back in tune, to the point where there's actually not a lot more adjustment in the E-string and I'm now finding myself looking at it (rightly or wrongly) with the same suspicious eye I viewed the saddle height with. I've included a pic of it as before.
I must say that all in - owning this bass has been nothing but a severe headache so far

There are also a few other things I'm not entirely satisfied about, like some poor finishing around the actual pickup cavities where it seems like it's been damaged when the pickups were originally installed. Not obvious from a distance but still noticeable up close. The bottom strap button is also screwed in at slight angle. Not perhaps 'major' issues but I feel like considering the bass cost me over £2000, I should be able to expect more. As I said I was pushing it to afford the bass in the first place but I figured that the joy it would bring me would be worth it since things haven't exactly been going my way this year - but it's ended up quite the opposite
Here are some snaps of my current worries (I apologise for the space they might take up, I had to edit/resize them quickly), again any further advice or comments warmly appreciated:
Saddle height as it is now:

Post-intonation:

Strap button:

Neck pickup left and right:

Bridge pickup left and right:
