iOS Bundle Identifier not being modified

Did you try to run the config locally, with the Bitrise CLI?

From the log it seems that your PlistBuddy call does not set the right bundle ID; maybe the Info.plist there is not the right one (not the one which is then used during the archive) or something similar, but the log line:

Provisioning profile "(DEV) Bitrise Test" has app ID "com.mnm.BitriseTest", which does not match the bundle ID "com.mnm.SpaceCells".

Means that the provisioning profile “(DEV) Bitrise Test” has a bundle ID “com.mnm.BitriseTest”, while the xcode project does not (based on the log the bundle ID of the xcode project is “com.mnm.SpaceCells”).