TL;DR: Those commands don't seem to do what you probably intend.
If you're trying to make at execute apt-get purge phpmyadmin -y from bash in 2 minutes, then your code will not do what you want it to do.
The command on the left of the pipe (|) has your here document as its standard input. That command does not even run until the shell has read your complete here document.
From 3.6.6 Here Documents in the Bash Reference Manual:
This type of redirection instructs the shell to read input from the
current source until a line containing only word (with no trailing
blanks) is seen. All of the lines read up to that point are then used
as the standard input (or file descriptor n if n is specified) for
a command.
A command with a here document is, in effect, just a single command that must be fully read by the shell before it is executed. In your code, the shell reads input until PMA_UNINSTALL appears on a line by itself. Once that has happened, the shell then uses the content of the here document as file descriptor 50 for the command bash /dev/fd/50.
That command does not even start a new instance of bash until the here document has been fully read. When bash does run, it runs this command:
apt-get purge phpmyadmin -y
Since the whole left side of the pipe including the here document has its standard output piped to at, the input at gets is the output of bash, which is the output of apt-get purge phpmyadmin -y. at then attempts to interpret that output--not your apt-get command, but its output--as a list of commands to execute in /bin/sh.
So this is almost certainly not what you mean to do.
I'm not sure why you don't get a shell prompt back right after entering that code. When I run it on a test machine, I get a shell prompt back in a couple of seconds. If you want to debug this, you can try running apt-get purge phpmyadmin -y interactively in bash. The way your code is written, that command runs completely before at returns to the shell (and before at can schedule anything). It would probably not be useful to debug this particular code further, though.