I think they may be referring to if someone accidentally changes the ordering, either by inserting a new variant between two existing ones or by shuffling the order of the existing variants the value can change and cause problems.
> The encoded value can change any time you re-compile your program
Any value (not just enums) can change any time you re-compile your program, if some programmer goes in and messes it up.
The real, much softer criticism would be that Go requires its programmer's to understand the potential consequences of inserting or shuffling enum values (where iota is involved). It's a much weaker case against iota than what they stated.