I don't know why they restricted mounts and yoshis from pipes, that's one of my main issues I have with smbx2. Thankfully there is a work around for this.
All you have to do is place a mount box by the entrance and exit of the pipe. Its a simple yet creative solution.
The egg box is just a custom graphic btw, but if you want to get more creative with the default mount box then I highly recommend using this.