Yes. If you are given extra time to take the MEE and MPT due to ADA accommodations, you may change your allotted time per question. Once in the Account View, click Edit Profile. Then on the page that is displayed, in the ADA time multiplier area, select the additional time you are permitted per question.
For example, if you receive time-and-a-half, select 1.5x. If you receive double the time, select 2x.
Save your desired time. This time will be reflected on your Timer.