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The idea is to have json generated files in the repo and to make sure that the correct version of re2c is used. The performance of JSON extension is dependent on their tools. In addition (and more importantly) there is a future possibility to increase the version to 0.13.7+ and use native UTF-8 re2c implementation which would simplify the scanner considerably.
However such restriction could be inconvenient for many users that prefer to use distro version of the re2c. For that reason the generation of re2c and bison files will be optional only if the user configure PHP with
--enable-json-filegen
option. There is absolutely no need to enable that option if the user don't want to change something in the parser or scanner (which will 99% of users and that 1% is probably just myself :) ). When the options is not enabled, the files in repository are used. That also means that there won't be any conflicts because the files simply won't be regenerated.