Well I guess there is something missing here , let me just say tell you what I know and lets us see if anything is missing
1- about the first issue … the flag (mutable-content),
iOS device are expecting the Notification messages to have the keys/values in specific format (capture 1 in attachment) …
Using backendless Messaging if you try to send all those flags mentioned in capture 1 (the documentation suggest that we need to prefix the flag name with “ios-”). … the received notification message dictionary is shown in capture 2 in same attached, here you see how the notification keys actually were formatted … those flags which were supported by the Messaging module were included in “aps” key after stripping out the ios- prefix, supported flags like: badge, content-available, sound,…etc)… however the rest (including mutable-content flag) were not added and I take it because Messaging Module is not configured to do that … (so to your point , yes it gets delivered but not included in the right place within the “aps” key) …some other dropped out flags also are key ones for formatting the notification message such as :body, title , subtitle …
This is my view , let me know if anything is missing .
2- Now about the other part (the “content-available” key) … this is actually linked to the point above , I thought it might be the source of conflict with not including the missing keys from the “aps" but further testing revealed that it might have nothing to do with it