From what I understand, different episodes from the UNIT era seem to have been written with differing assumptions as to when those episodes took place relative to the audience's "present-day." But I think the idea was that by alluding to a female Prime Minister, that particular serial was supposed to be seen as taking place in the near future.
Personally, I just say wibbly-wobbly-timey-whimey and let it all be.
ETA:
To digress just a little bit...
One of the things I thought was hysterical about RTD-era
Doctor Who was that, every season, they'd manage to kill or overthrow the Prime Minister or surrogate. The Slitheen killed Tony Blair in Series One; the Doctor overthrew Harriet Jones in "The Christmas Invasion" and the Cybermen killed the President of the People's Republic of Great Britain in the alternate universe in "Rise of the Cybermen;" the Master was elected Prime Minister, assassinated his entire Cabinet, and then was killed by Lucy in "Last of the Time Lords." And the Daleks killed Harriet Jones and shot down the sitting Prime Minister's plane in "The Stolen Earth."
And then, during the specials year, Prime Minister Brian Green was forced to resign at the end of
Children of Earth while the Master took over President Obama's (and, presumably, Green's successor's) body in "The End of Time, Part One."
It was just such a great running gag, and I'm kind of sad no Prime Ministers or substitutes were harmed during Series Five.
It is sort of funny to think of this unnamed PM as Thatcher, given the later history of the writers and producers with her, i.e. the rather candid criticism of her policies in the McCoy years.
