This is one of the problems/limitations of using the Digital output format = Auto setting ("Automatically transcode the source audio to the highest detected Dolby level of the connected device") in the 4800/4802: you may/can get empty channels, incorrectly mapped channels, volume level issues, broken audio, stuttering audio, audio delay/sync issues, etc, all either preventing upmixing/surround processing in a TV/AVR/SB or making it problematic to do so.
Roku (or any other lower-end streaming device manufacturer) isn't going to provide many (or any) granular controls over how its Dolby decoder (and encoder) operates: in fact most devices with a Dolby decoder don't even allow the user to disable it (e.g. FireTV OS, TiVo Stream 4K), and otherwise only allow settings like volume leveling/dialogue enhancement (FireTV OS) or to restrict the Dolby codec level (e.g. FireTV OS - DD/DD+/Best Available) for output (the 4800/4802 has the same ability).
The fact that Roku allows the user to put the Dolby decoder into a Passthrough mode at all (though not completely disable it, and its not completely passthrough) is very unusual - even the Nvidia Shield 2019 only allows the user to either enable or disable their Dolby decoder and otherwise only has one or two indirect settings for it (e.g. matching Dolby & PCM volume, or not resampling for output), though its possible to manipulate the Dolby decoder's behavior through other audio-related device settings.
So yes, the Roku could (and does) identify PCM 2.0 source audio, and when using Auto mode then transcodes that to the highest detected/configured Dolby level for output.
If you don't want any transcoding (and most users are very rarely ever going to want this) you'll want to configure Passthrough mode and use your TV/AVR/SB's upmixing/surround processing modes.
Since you are aware of Roku's AAC support limitations and want/need AAC 5.1 you can either:
1) Wait indefinitely for Roku to reduce/eliminate them (e.g. Transcode 5.1 AAC to Dolby 5.1 or passthrough AAC including 5.1) <-- very unlikely to happen for any current or even future product
2) Re-encode your AAC-encoded media files to EAC3/AC3 (would have much better support in any/all streaming devices) <- a pain, but relatively easy
3) Use a different streaming device(s) with better AAC support (e.g. NS19) <-- a pain, but relatively easy