Although Mailspring does (as you’ve spotted) allow aliases for an account, it always seems to use the main email address for the account when replying. As you say, it would be nice if it would detect the address the original email was sent to and use that address to reply from - it would make aliases a more integral part of the app rather than a tacked-on extra. However, the ability to create new aliases on-the-fly (which is effectively what you’re asking for) might cause more trouble than it’s worth with e.g. BCCed emails or mailing lists, where there might be all sorts of email addresses in the original email that you wouldn’t want used as aliases! (In your case, your aliases are all from the same domain, by the sound of it, but that’s not the case for everyone and so Mailspring can’t assume that to be the case. Perhaps a wild-card fallback alias might be possible, but it’s probably an edge case because most people probably don’t create new identities on the fly as you seem to.)
Perhaps raise this as a feature request in the relevant area of this forum? I suspect a feature “Use alias as From address when replying to emails” is easier and more likely to happen than “Auto-create aliases from address in original email” because of the false-positive issues mentioned above, but it’d be worth listing both parts IMO.