I´d advice to select a "daughterboard" which come in several formfactors, and contain the CPU, RAM, Flash
this components are today mostly BGA, very fine pitch, Multi layer boards >=6 Layers, a lot of nets that need length matching, diff pairs and maybe controlled impedance
and design not a "Mother"-board, but a "Carrier"-Board containing Power and Connectors / Peripherie to outside which can be 4..6 Layers and Compnents with pitch that can be still handled maanually if you got steady hands.