I only contributed some minor fixes to SQLite, but I'm not a real maintainer. I don't follow the development of DBD::SQLite closely, so I don't know the implications of always enabling the tokenizer. If there are no side effects other than compiled code for a feature that is likely to be unused, I don't think the real maintainers will object.

I would write a mail to Kenichi Ishigaki with the proposed change and the idea why this change is harmless. Also, the changed Makefile.PL resp. the patch against the current Makefile.PL is more likely to get your changes into the next release.