Generally you have to test your equipment in its "worst" configuration. There are a few ways to handle this.
Delete boost mode. Is it necessary for the product?
"Delete" the boost mode for the purposes of the EMI test. In production, you can have some way of enabling boost mode with a note in the manual that the equipment is non compliant in the boost mode.
Negotiate to have the test done in normal and boost modes. You'll get a test report that may show "failures" in boost mode. Do as above. Put an asterisk on you EMI compliance.
See what it would take to make the equipment compliant in boost mode- is it really hard?
Good luck.