Chris, have you specifically asked the manufacturers what quantities you need to get those prices? Those don't sound like "onesie-twosie" prices. Those sound like prices they would quote for larger production runs.
If you are only doing this for your own use, there are many options, from mdavej's beloved JP-1 compatible remotes, to Logitech Harmony, to Universal's stuff. Not sure that going full custom hardware is an option, unless you want to spend frightening amounts of money. Many of the existing remotes have enough programmability that they should meet your needs. If you need something entirely different than a regular remote button layout, why not try programming a tablet, smartphone, ipad, ipod, etc.? If you have demonstrated enough technical prowess to create something that mdavej would want to steal, whipping up a remote on one of those platforms should be a snap!