Clockwork is mainly for reducing your abilities' cooldowns (i.e. Trampoline! and Brambleboom Seeds, with the A ability being affected by the reduction in the 2.2 update) and for amplifying crystal damage. Halcyon Chargers are an option as well.

It is quite useful to get that extra speed and having that 'Sprint' ability available early-game, but I personally don't see a need for those, unless you're willing to replace Clockwork with Halcyon Chargers. Petal's Trampoline! with some cooldown reduction is good enough to escape, but having boots is definitely an option.

Having an Aftershock is just for doing more damage against tanky heroes, especially if your munions don't do much damage and you want more. Mastering Petal with an Aftershock can be quite difficult since you have to plant seeds very often to deliver amplified basic attacks, but is otherwise a good item choice.

It is true that Flicker's Mooncloak doesn't affect Petal's munions, but she's still able to participate in ganks with her teammates during the effect. She just has to be in the back, or in an area where she and her munions can't be seen if you're waiting to ambush the enemy team.

I updated the guide anyway, so thanks for letting me know!