I don't understand why a timer can't be used to count down from 45 and stop every time there's a stoppage in play. The whole thing is absolute bollocks tbh, football have become 94 minute games as that one nearly always comes up even if there hasn't been any stoppages.
They do use a timer, the referee has two watches - one counts down (usually) and the other is kept on the normal time - the count-down is stopped whenever a stoppage in play requires time to be stopped (sounds funny...). What people on the TV just gives off the wrong impression of how football is time-kept - remember ruggers has longer stoppages for conversions and stuff.
The FA do not give any time suggestions (as far as i know, but then again, i'm not refereeing at the top and they give them all sorts of crazy advice...) If play is stopped for anything ceremonious then play will be stopped - free-kicks around the area, subs, mis-conducts etc, and the ref will then re-start his timer on at the restart of play. When he notices (or gets told by the 4th) that it's been 45 mins since K.O he'll tell him,at least, how long he still has on his countdown. Of course, when players take a little too long at a goal-kick, throw etc, the referee will use his discretion and determine what is acceptable - if too long, warning then a caution, or maybe just a caution, then just play for a few moments after the count-down has finished.
You'll often find referees not blowing up during, what could be, a promising attack, and if a goal is scored,the ref will play a minute or two over his 'added time' to not give the impression he 'only played on until that team scored' - i.e 'cheating'. Why referees blow up just as a goal kick is taken (i know it's not been mentioned) is weird, the ball doesn't even have to be in play for a half to finish.
Someone said it, the ref is sole time-keeper, how he keeps it, and what he deems to be a sufficient stoppage in play is purely up to him (obviously knowing the general stoppages in play that require time to be stopped). Sky/TV laws are totally different to FIFA's law book, and remember, one of the countries top pundits/commentators is Andy Gray...and he's fucking thick when it comes to the laws of the game!