I think your wish translates into a customizable selection for the INBOX folder.
That would be technically possible, independently from whether deltachat is able to properly sort and manage the chat messages out of the email messages in INBOX https://github.com/deltachat/deltachat-core/issues/422
One drawback of selecting a different folder instead of INBOX would be that with deltachat being configured for a (different) alias and INBOX, deltachat can not easily detect your “email approved contacts” (those that have been emailed by you or your known contacts).
Properly determining the email approved contacts, and a size limit for chat messages, is important because it allows to get rid of always having the annoying “Do you want to start a chat” prompt --that is also silent and thus easily missed–, even if an already known contact is sending you a chat message for the first time.
I understand, that using an alias can be a workaround for current or future problems with deltachat not being able to manage the chat versus email message selection properly, but think that exactly solving this problem well is what will make deltachat really easy to use.