I'm not sure if they've made it more difficult in a while -- they disabled mounting /system read-write but I was still able to copy the block device to another host, modify it, and copy the modifications back. At one point they disabled opening the block device (which was a partition) read-write so I had to open the containing block device (which was the whole disk) read-write and add an offset.

ChromeOS uses dm-verity to prevent this from being an issue, but I'm not sure Android does -- so you should be able to flip some bits on disk without being noticed !