Currently the skill is automatic and, according to in-game help, increasingly increases your melee combat effectiveness with the duration of the fight. While not knowing how exactly this is being done in-game (probably just an increasing % of damage added as a bonus to each attack), I suggest this skill to be changed into short-term affect such as poison.

It would grant you HR/DR, in somewhat small amounts, with every tick spent in combat. The ratio would generally depend on skill proficiency % and may be somewhere within the range of 1 point for every 30-100 ticks. Essentially, inside a combat routine, you'd check if you're still in combat, apply/refresh the affect with updated numbers and duration similar to 10 seconds.

PS - IDK if you're yet out of available affect flags.

Battle rhythym and combat attunement are both incremental based on combat ticks. It is slow to ramp up, similar to poison although not quite as slow, and then it ramps down while out of combat. In essence, it is extremely similar to what you've suggested except it is built directly into hitroll/damroll modifiers instead of as a side-effect that boosts them. This is because they are % based bonuses to your current hitroll/damroll, and it was simply an easier implementation this way.

In regards to the PS, we don't need to worry about those kinds of issues. If we legitimately have a need for 1000 affect flags, then we can use 1000.