Strangely enough, the advice that you got is basically correct but you probably could do EQ to correct for the different in-room response of the floor-standers mounted in-wall. However, this would take some measurement/EQ equipment (such as a Behringer DEQ 24/96 UltracurvePro with ECM8000 calibrated microphone) and a little time to get the fronts rebalanced. You would probably need to leave the EQ on all the time when using the system with speakers mounted in-wall.
What is happening is that the diffraction of sound from the edges of the speaker cabinet change when you mount speakers flush in-wall. The floor-standing speakers were designed and balanced for non-in-wall use.
Chris