Common mode (CM) and differential mode (DM) filters components reduction
The common-mode filter will change to a first order filter without the capacitors. That might be satisfactory but you would have to measure the change of EMI and decide if that  performance is sufficient for you.
Positioning the differential capacitors in a less-than-idea layout is making that filter worse, but here you also need to consider the stability of the DC/DC.
You are making your design worse, and cutting margins. If you cut too deep you might fail regulatory testing, and/or have a system that will get unstable in elevated temperatures or as the capacitors age.
What you are doing introduces risk, that can be mitigated with additional testing. Doing this is the wrong approach to low EMI, but it might be &quot;low enough&quot;. That is up to you to decide.