Are there different ways to pronounce certain hiragana and katakana?

2 comments

1. This has nothing to do with your elaboration, but on a technicality not related to your question, yes certain kana are pronounced differently depending on context because of stuff like [devoicing](https://youtu.be/iYQM7BhJJns).

   As for “ja” and “jya” it’s just a different system of rōmaji. (Also, yes, “RŌMA,” not “ROMAN”). The inconsistency of rōmaji usage is one reason why people should drop it immediately. As far as rōmaji keyboard input, “ja” and “jya” are fine, but as far as Japanese people are concerned, the sound of “じゃ” is just “じゃ.”

2. In general they’re always pronounced the same, but some times euphony occur for certain sounds. The example you gave is pronounced “Ji Ya.” If you want “Ja,” it has to be written like this じゃ. The small や is necessary for that distinction.