Scenario: Start out in a fresh instance with Tinkers Construct installed and Crafting Tweaks not installed, with no configs generated yet.

This line right here will generate the config option for the Pulse, using PulseMeta.getEnabled():
ForgeCFG.java#L52

However, PulseMeta.enabled has been set to false because the mod wasn't loaded here:
PulseManager.java#L148

...resulting in the value for the newly generated config option to be false despite defaultEnable claiming the default would be true. This makes it painful to add Crafting Tweaks to a pack later on as users have to specifically enable it in the Tinkers Construct config.

I believe this could be easily fixed by making ForgeCFG.isModuleEnabled use meta.isEnabledDefault() instead of meta.isEnabled() for the default value of the config option.

You are correct, good catch. I actually had Arkan implement the defaultEnable for exactly this reason, but the old config implementation never got updated.