MPSeal can't seal MPs that depends on a .mpb, but FastSeal can.
And FastSeal actually doesn't even care about referenced mps at all, so you don't need the referenced MPs at all and you can just seal your MP like this :
fastseal.exe "C:\MyMPs\my.custom.MP.xml" /key "c:\MyMPs\mykey.snk" /company "MyCompany"