These pronounciations are for the International radiotelephonic spelling alphabet, often referred to as a "NATO Phonetic alphabet". For numerals procedures vary slightly, and they've chosen IMO. The sounds are chosen to try to maximize the chance that two people who know this system, even if they don't speak any shared languages, will successfully communicate the symbols intended, so they're not about how you might pronounce these words in any particular place, but rather a plausible pronunciation everybody can approximate and understand.

This makes sense. "R" is throaty in (e.g.) English and French, and a tap or a trill in many other languages.

Allow me to be pedantic: In some dialects of english.

I thought 5 was supposed to be pronounced "fife" but this page only seems to half say that. ("faif" in the first row, but "five" in the second)

IIRC in WWII the UK settled on 'fife' and nine, while the US went with five and 'niner'. Arthur C. Clarke's novel Glide Path described the adoption of fife.

Or… England?

Ouch. My stereotypically-American US-centric bias is showing :)

Old England.

With the new non-rhotic affectation.

Which is really getting out of hand, to the point that some English speakers are starting to sound positively French: ‘cweam’ instead of ‘cream’ the same way the French turned ‘rex’ into ‘wa.’

I blame the EU.

I was tempted to say "parts of England"... but I wanted to mean "parts of the united Kingdom"... so... you are right :)