Re: Chips in the substrate
Yes, it can be done. Inserting resistors and diodes is common; inserting chips and capacitors I've only personally seen once. But then I worked in the software side of a defense company, so I had little exposure to this stuff. Search on the website of a company like Curtis Wright and if you can find a photograph of a processor board without metalwork, then you are likely to only see large BGA's and a few interface chips (the devices that need the cooling) and an otherwise bare PCB surface (to allow a ground plane on each side of the PCB stack to cut down on EMC.)
Your real question should be can it be done cheaply enough, with the follow up of what is the budget for this information?