[Google Pixel XL Questions & Answers] Scott:
No, the unlocking and rooting is not the issue here. Its almost like you have a corrupt system paritrion.

Hopefully its just software but to check you need to reflash the lates factory image to be sure...

Here is the part that is concerning to me....

11-19 15:11:25.071 14609 14629 W StorageManager: Could not read /sys/block/mmcblk0/size
11-19 15:11:25.071 14609 14629 W StorageManager: java.io.FileNotFoundException: /sys/block/mmcblk0/size (No such file or directory)
11-19 15:11:25.071 14609 14629 W StorageManager: at java.io.FileInputStream.open(Native Method)
11-19 15:11:25.071 14609 14629 W StorageManager: at java.io.FileInputStream.<init>(FileInputStream.java:146)
11-19 15:11:25.071 14609 14629 W StorageManager: at java.io.FileInputStream.<init>(FileInputStream.java:99)
11-19 15:11:25.071 14609 14629 W StorageManager: at android.os.storage.StorageManager.readLong(StorageManager.java:944)
11-19 15:11:25.071 14609 14629 W StorageManager: at android.os.storage.StorageManager.getPrimaryStorageSize(StorageManager.java:935)
11-19 15:11:25.071 14609 14629 W StorageManager: at com.android.settings.deviceinfo.StorageSettings$SummaryProvider.updateSummary(StorageSettings.java:492)
11-19 15:11:25.071 14609 14629 W StorageManager: at com.android.settings.deviceinfo.StorageSettings$SummaryProvider.setListening(StorageSettings.java:484)
11-19 15:11:25.071 14609 14629 W StorageManager: at com.android.settings.dashboard.SummaryLoader.setListeningW(SummaryLoader.java:192)
11-19 15:11:25.071 14609 14629 W StorageManager: at com.android.settings.dashboard.SummaryLoader.-wrap2(SummaryLoader.java)
11-19 15:11:25.071 14609 14629 W StorageManager: at com.android.settings.dashboard.SummaryLoader$Worker.handleMessage(SummaryLoader.java:253)
11-19 15:11:25.071 14609 14629 W StorageManager: at android.os.Handler.dispatchMessage(Handler.java:102)
11-19 15:11:25.071 14609 14629 W StorageManager: at android.os.Looper.loop(Looper.java:154)
11-19 15:11:25.071 14609 14629 W StorageManager: at android.os.HandlerThread.run(HandlerThread.java:61)

It looks like its having a hard time reading the block 0 partition. Which then "seems" to be causing root assignment issues for other files.

I would wipe and test again.

And then there is this...

E DropBoxManagerService: Can't write: storage_trim
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: java.io.FileNotFoundException: /data/system/dropbox/drop24.tmp (Read-only file system)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at java.io.FileOutputStream.open(Native Method)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at java.io.FileOutputStream.<init>(FileOutputStream.java:221)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at java.io.FileOutputStream.<init>(FileOutputStream.java:169)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at com.android.server.DropBoxManagerService.add(DropBoxManagerService.java:250)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at com.android.server.DropBoxManagerService$2.add(DropBoxManagerService.java:129)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at android.os.DropBoxManager.addText(DropBoxManager.java:282)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at com.android.server.MountService.onEventLocked(MountService.java:1212)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at com.android.server.MountService.onEvent(MountService.java:1045)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at com.android.server.NativeDaemonConnector.handleMessage(NativeDaemonConnector.java:150)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at android.os.Handler.dispatchMessage(Handler.java:98)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at android.os.Looper.loop(Looper.java:154)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at android.os.HandlerThread.run(HandlerThread.java:61)
11-20 03:06:00.994 1043 1103 E DropBoxManagerService: at com.android.server.ServiceThread.run(ServiceThread.java:46)
11-20 03:06:01.004 2393 20514 W FileUtils: Failed to chmod(/data/user/0/com.google.android.gms/files): android.system.ErrnoException: chmod failed: EROFS (Read-only file system)

This also goes along with my theory that there is corruption on your phone. There are other instances for other applications as well.

A full system image with wipe "should" fix it unless its an actual hardware failure.