Yes, the $5250 limit still applies.

To be specific, you can have the plan trustee withhold the full $10,500.  However, when you file your MFS return, the maximum you can exclude from income is $5250, and the overage will be added back to your taxable income (there is no additional penalty).

This means that if you think you might decide to file jointly, I would take the full amount allowed (but not more than the cost of care, of course) because if you do file jointly, you get the full benefit, and if you file MFS, you won't be any worse off than if you had just taken the lower limit.  If you are sure you will file MFS, there's no point in taking more than $5250.