Re key locking and remote entry - AFAIK the Mk2 and Mk2.5 have the same system, but the PCM’s are slightly different, as the Mk2.5 1.8 version has added VVT control.
I need to qualify that statement I made about the depth of water, I haven’t poured water in my or anyones car to find out, the 3" is a guess, based on the fact that the PCM is located under the sloping part of the footwell about half way up, in a compartment about 10-12" square and covered with a gasketed lid which is also permanently fixed with ‘break-off’ bolt heads’ which have to be chiseled to make a slot with which they can be unscrewed.
Also - I’m assuming the car is on a level base, if it’s facing downhill, then the story could be worse! However, if there was water in the footwell, even if it didn’t reach the PCM enclosure, it won’t do the floor any good, and particularly seat mounts, which might raise safety issues. If - as you say, the seller now wants a thousand for it, then I personally would want to see the engine running, and a new battery fitted, and while they won’t like it, either an MOT and Tax if it’s driveable, or you’ll have the added expense of getting a truck and trailer to shift it. Afer three years non-use, I wouldn’t like to drive it without an MOT pass.(Even with a trade plate)
As you say it’s been stood for three years then I would make the assumption that you may have to spend several thousand on it to cover potential problems, while you can buy a running Mk2 for less than the eventual cost - check out the cars for sale on here, ebay and privately. My advice would be - walk away, and find a roadworthy car, Mk1 or Mk 2. Dreams are one thing,. reality is often harder to bear, but you should always face reality, as it’s the only sensible option.
I’m not recomending them - though some local members would - but there’s an outfit up here at Shardlow just outside Derby who buy scrapped Mx’s (usually insurance write-offs) who then repair them and resell them in a roadworthy condition. They only do this if the basic car is repairable, otherwise they break them for spares, but a comparitively new car can be bought for far less than the market value of a good car and it’s worth considering. Most write-offs are due to front or rear end collisions, and as long as the rest of the car is all right, then it makes sense to repair the damage and move them back into the market. They also sell spares, but not front and rear ends, as they need them for the next repair! I’m told they currently have a Mk3 CC for far less than the market cost, though I’m not suggesting you go for it. (it may be sold already anyway!)
They are - P H Sportscars, British Waterways Yard, Cavendish Bridge, Derby, DE72 2HL 01332 799298
Footnote - PCM is short for Powertrain Control Module, the Mazda equivalent to ECU.