If I apply for your certificate of eligibility online, and it is approved, the email I receive from the Immigration Bureau itself is the certificate of eligibility. Once I forward this to you, and you show this email from me at the Embassy in your own country, your visa will be issued. You also need this email I forward to you when you enter Japan and receive your new residence card.
Please think this:
When you go to a concert, you quite often show your ticket on your smartphone. When you go to a sports event, you show your ticket on your smartphone at the entrance of the arena. When you fly, your boarding pass is on your smartphone. Hence, the certificate of eligibility can be in your smartphone.
A client I recently forwarded the email from the Immigration Bureau asked me whether his visa would be truly issued by showing the email I forward to him more than a few times. In the end, the visa was issued, he was admitted, and his new residence card was issued by email.
Even so, if you prefer the conventional certificate of eligibility, in other words, a printed certificate, please let me know. It still is available if you wish.