A minor thought on this - Torchwood is funded directly by the Crown, presumably the same pot of money that pays for the upkeep of the Royal palaces, the Queen's day to day expenses, etc. It's presumably a black item in the budget, and must be pretty difficult to conceal, especially with a new base to equip.
There's a summary of royal finances etc. herehttp://www.royal.gov.uk/TheRoyalHousehold/Royalfinances/Overview.aspx
One way to keep the costs down would be to find a suitable location that is already owned by the royals and not actually in use. Not impossible, I'd imagine, since they own quite a few properties around the country. I don't have a list, maybe someone else can make a few suggestions. Presumably in the Cardiff area, given the presense of the Rift, but they may be able to base themselves a little further away without cutting themselves off from it.
A final thought, if you don't like that idea - given all the explosions etc. towards the end of S2 there must be lots of rebuilding going on around Cardiff, and lots of derelict buildings. Shouldn't be too hard to find a site.