Someone tell me if I'm wrong here, but I just read the Google support page discussing the changes, and here's what I came away with.
Permission groups are new. If you grant permission for an app to have access to the features controlled by that permission group, then the app has access to all of them. Using the SMS example, if a developer requested the SMS group permission, the developer is asking you to allow the app to do all the things listed under that group. That would include reading SMS and sending SMS messages, among other things. If an app requested the SMS group, and you installed the app, even if the app previously only read SMS messages, it still had permission to send them. A future update may also send SMS messages, but you've already approved that action by installing and manually approving the previous version of the app. Where it gets dicey is if a new permission were added to a group. For example, if a delete SMS feature were added to the group, I don't think the Google page discusses whether that new permission would need to be approved.
An app developer can still ask for individual permissions, like reading SMS messages. If a future update wanted the ability to send SMS messages, they would still have to ask and the app would not be auto-updated. Or, if the app developer later decided he/she wants to add the SMS group permission request, that download would require manual approval.
I don't think there's anything nefarious going on here. You just need to be aware of what permissions you're granting an app. If you grant an app permission to send SMS messages (whether it's via an explicit request for that ability, or whether that ability is granted via a permissions group), don't get upset when it does send an SMS, even if that feature isn't baked in until a later update. As far as I can tell, no app is being granted permission to do something you haven't already given it permission to do. Except for internet access.
The internet access permission being demoted to a secondary permission, on the other hand, might be cause for worry.