After having trouble with incorrect initial configs, I recommend the following:
When generating a default configuration file, leave all non-essential lines (those that are not intended to be tuned by average user) commented out.
Remove all non-essential lines (those that are not absolutely necessary) from sample configuration files. Remove directive descriptions as well, or keep them minimalistic. Make it clear in INSTALL documentation that all sample configurations are only for testing whether the built binary really works, and they shouldn't be used as a basic template for further adjustments.
This should help to prevent situations when an aged configuration file lacks some new directives, or contains some "magic" values that aren't appropriate anymore.
As far as I see it, most users will never change servo parameters, communication intervals and many other things. Currently, with all directives uncommented by default, they add nothing to the resulting state as long as their values remain consistent with the code, but they will impede new default values from coming into effect whenever those are introduced. If all defaults were commented out, the new defaults would took their place seamlessly. Anyway, even if those new values broke compatibility for some users, these users would be able to uncomment their previous defaults to check if that restores normal operation.
One thing to add would be that the file ptpd2.conf.default-full that's part of the distribution, is generated by ptpd itself and contains all possible settings explicitly set to their default values. ptpd2 --default-config / ptpd2 -O gives you this output and apart from actual bugs (like the one you raised recently), when used, is no different to not setting anything.
The idea of the default config file is that it's a config file containing default values, not the default config to be used.
But anyhow, we get your point, ptpd needs some housekeeping, but this is a hobbyist project with no backing so we do what we can in our free time. The situation has greatly improved in 2.3 anyway, previous versions didn't even have config file support and we literally ran out of one-letter arguments, upper and lowercase :)