6E1 page 347 says that you can give a power continuing charges to avoid expending a charge each phase with time limit, and it says the GM typically caps the value of continuing charges at -0. In this case does capping it mean it doesn't become more of a limitation or it doesn't become an advantage or both?

It primarily means it doesn’t become more of a Limitation, but it could also apply to the Power Modifier when it’s an Advantage. The primary idea here is not to make Time Limit cheaper once you’ve established it should be an Advantage for the power in question. Whether the GM also doesn’t want it to become more expensive because of Continuing Charges is up to him. Personally, I probably wouldn’t worry about it unless the value of Continuing Charges became pretty large (+1 or more), but each GM has to decide for himself where the campaign balance tipping point is for his game.