My suggestion would be to open a new support ticket here https://support.advancedcustomfields.com/new-ticket/ and to also report the problem to the developer of the other plugin. Like I’ve said, I’ve never used the other plugin, or even used custom templates for post types other than pages. I have thought about it but more than likely did not find a plugin that I trusted well enough to handle the job so I chose a different direction like ACF fields to make choices and different template parts based on those choices.
The new version of ACF includes support for whatever it is that WP is doing and also to be backward compatible with WP Core. Between it being new in ACF and the need to account for a plugin that I’ve never worked with, I doubt I’d be able to figure out how to work around the problem. You’ll probably need to build you own custom location rules just for working with the other plugin in WP < 4.7. More then likely, it probably means reworking something for WP >= 4.7 since any plugin that’s currently doing this is going to be obsolete.
