Absolutely. The only way we can be sure that this will be fixed by 2036 is by introducing a new NTP version that doesn't have this problem. Anything running the current version (which could be seen on the wire) would be considered broken.
NTPv4 introduces a 128-bit date format: 64 bits for the second and 64 bits for the fractional-second. The most-significant 32-bits of this format is the Era Number which resolves rollover ambiguity in most cases. According to Mills, "The 64-bit value for the fraction is enough to resolve the amount of time it takes a photon to pass an electron at the speed of light. The 64-bit second value is enough to provide unambiguous time representation until the universe goes dim."
Luckily remediating this is relatively easy: Use some indicator for "certified 2036 proof" NTP clients that's visible on the network (a different port, an extension, ...), then observe the network to find legacy traffic.
Won't catch absolutely everything (e.g. local containers), but will probably get pretty close. Especially if modern NTP client versions have some way to resolve the ambiguity, e.g. a hardcoded "it's after 2020".
