I genuinely see no factual or social difference in the domains; tuta.com is a new domain even; and in the world of E-Mail that may even be a problem in rare cases.
Realistically tuta.io is shorter than tuta.com. The .com TLD is not better than any other, and all TLDs; including gTLDs are 100% valid for email addresses. Any Software or Human entity that assumes otherwise is doing things incorrectly; and should be promptly complained about loudly.