So I just wound up blowing away my pmserver and started fresh. Not sure why the dropdown never showed the PHAR file. Once I created a new server, I was able to see the DEV PHAR file in the drop down. I will mark this as closed.
I compared the server.config files between the old pmserver and the new one… there was a difference in that the PHAR file was specified in the new server.config file.
mc@mc-linux:/var/games/minecraft/servers/pmserver$ cat server.config
mc@mc-linux:/var/games/minecraft/servers/pmserver$ cat ~/PocketMine/server.config