As noted in the issue, it's by design, since Construct is detecting your project as compatible with modules and switching it over automatically.
The option will be removed soon anyway - it only exists for a backwards-compatibility grace period for addon developers to update their addons if they need to change anything, and it's been around 4 months now, which I think is long enough for anyone who's going to publish an update to do so. If you still need it for a third-party addon, you should get in touch with the addon developer ASAP, as the option is going away.