The issue discussed above was that the channel order passed by Logic to the plugin didn’t match the channel order it declared in its kAudioChannelLayoutTag for certain Atmos layouts. We reported this issue to Apple and have not heard back.
I think that the behaviour you’re describing is the intended behaviour of the JUCE channel remapping.
The JUCE channel order should not be expected to match the order of inputs provided to the plugin. Although Logic uses the order LS L C R RS LFE by convention for display purposes, in Logic 10.6.3 I see that Logic provides channels a test 5.1 plugin in the order specified by the kAudioChannelLayoutTag_MPEG_5_1_A layout, specifically L R C LFE LS RS. This isn’t set in stone - Logic could also choose to use kAudioChannelLayoutTag_MPEG_5_1_B, and the channel order would be L R LS RS C LFE instead.
To be as clear as possible: the channel order that Logic displays in its UI does not necessarily correspond to the channel order that it passes to hosted plugins.
Perhaps you could approach the problem in a different way. For example, if you know that you want to process the left surround channel, you could use getCurrentLayout.getChannelIndexForType (AudioChannelSet::ChannelType::leftSurround) to find out the channel index for this channel type, and then read from that channel index.