Politely say "I don't care what you think but I won't change anything" is perfectly fine in Japanese culture. Taking an issue privately instead of showing disagreements in public is also perfectly fine for Japanese people.
The issue has nothing to do with Japanese culture, but with how you work with a community of volunteers over the web. "Let's jump on a call" is what you say to a coworker, not to a volunteer in an online community.
Let’s jump on a call is something you say when you feel that the tone and intention of your communication is getting lost in text. And whether it’s common in all cultures or not, tone and intention getting lost in text is universal.
The issue has nothing to do with Japanese culture, but with how you work with a community of volunteers over the web. "Let's jump on a call" is what you say to a coworker, not to a volunteer in an online community.