I'm not an admin, but I subscribe to several groups.io lists in daily summary mode, and I reply to messages all the time, either privately or to the whole group. Here's what I do.
When I click, in the email, on the link for the message I want to view, I'm taken to a web page that contains the message and all replies. Below the message and each reply, among other things, is a Reply link. When I click on this, it opens two edit fields: one with the subject filled in and the other for the reply. After I type my message, I navigate to the Private button and press it. Then, I navigate back to the Send button and click on it, and that does it. I hope I've been helpful.