A UI issue for you...
iMac Retina 5k 27-inch Late 2015
OS X El Capitan 10.11.3
Alfred 2.8.2 (432)
Reproducible: Yes
Aways: Yes
Tried on other machines: No
Steps to reproduce:
Open Alfred preferences
Click the Features tab
Click the Terminal / Shell section
Change the Application dropdown to be Custom
Close preferences
Open Alfred preferences
Click the Features tab
Click the Terminal / Shell section
Change the Application dropdown to be Terminal
Results is that you see parts of the Default Results section's UI in the Terminal / Shell section's UI.
I would attach a screenshot, but it's either mindbogglingly complex to do so, or it's just not possible.