Not clever or experienced enough to comment on the ECU's but know a wee bit about Police and their vehicles.
Auto/manual varied from force to force. Most of the Met/TVP larger (Omega sized) vehicles were auto's for some reason whilst the more provincial forces (like mine) were manuals.
As already stated by others, ECU's tended to be stock but there were some adapted ones out there from the factory. I know of at least one Senator and one Omega that was at the Scottish Police College that were heavily modified from the factory and used as test beds. If they broke, they were trailored back down south for repair and evaluation and return.
Also had a FWD Ford Escort (when they were brand new(ish) fitted with four wheel steering (again from the factory) and experimental switchable mechanical/electronic ABS for use on the skid pan/manouevereability course. When that car had done its time, it was sthill sawed into large chunks on the premises before scrapping as it had no chassis number from new....
Omega was initially introduced in the UK as Police use for a few months before sale to the general public in order for miles/abuse to be racked up and returned down south for repair and evaluation etc as previously.
As to cars being uprated, alternate front exhaust downpipes (look at the price each in the TC book - you will get a shock), heavier suspension, additional wiring to accomodate roof lights etc and radio kit, beefier alternator/battery to cope with the load and alternate diff ratio, sometimes (but not always) with LSD.
As to being well maintained, I can only suggest that they are/were 'regularly' maintained. The in house w/shop techs were/are on pay rates much less than commercial shops and corners get cut in order to get turn around times done. If a cover can be butchered to allow easier regular access rather than removel thus saving a half hour each time, well, add it up onto monthly bonus.....
edit for spilling mustooks....