MS-IME or Google Japanese Input. (whatever)-Mozc on Linux. Use "IME On" mode for Japanese, "IME Off" mode for alphanumeric text inbetween.

  "shio ha natoriumu[Space][Return][ImeOff](Na)[ImeOn] to enso[Space][Return][ImeOff](Cl)[ImeOn] kara dekite imasu[Return]"
  -> "しおはなとりうむ(Na)とえんそ(Cl)からできています"
  -> "塩はナトリウム(Na)と塩素(Cl)からできています"
  (NOTE: spaces added for legibility)

Most Japanese users use this "romaji" input - which is more vibe heuristics based and not highly consistent with existing romanizations hence the change. Some use "kana" with full 51 Hiragana symbols on JIS keyboard(with ろ/backslash/underscore key to left of RShift, which makes it incompatible with ISO). I think "most people don't do this anymore" remarks refer to the fact that everyone's on the phone, and uses the "flick" input.