Fusing electronic platforms into one IC board
It is highly unlikely that you will be able to obtain the "VHDLs" for all these types of components as that is the proprietary property of the various chip manufacturers. So unless you have a huge money bucket and plans to staff up a sizeable IP design team you are going to be better off to stop thinking of replicating the whole design into some FPGAs.

You mention a RaspberryPi. The SOC type processor on one of those boards would require FPGAs that would cost more than 100 times what the RPi processor component costs -- even if you could somehow talk Broadcomm into giving you the "VHDLs" for the device. So once again as you will realize that this a killer of an approach.

You mention that cabling together a bunch of existing modules is ugly. That is fine but it is a great way to prepare a prototype proof of concept platform. Once you have that developed enough to fully understand all your components and software requirements the proper next step is to design your own board and packaging to accommodate the various needed components. Be prepared for a sizable investment of money, time, expert consultation and government agency approval processes.