this was happening with the older betas, and continues on the newest one.
exporting videos with object masks via media encoder gives warning that masks are offline, and exported media does not contain masked layer at all (as if the layer visibility was toggled off).
this is not an issue when exporting each video on its own directly thru premiere.
System info
Application: Adobe Media Encoder (Beta) v26.0.0.36
OS: macOS v15.6.1, RAM: 16.00 GB GB, CPUs (logical): 8