In Configuration Manager 2012 R2 a new variable was introduced to help us solve an issue with installing applications in a task sequence on new computer with SSD drives where all the networking components are not loaded when the Task Sequence tries to access the MP which results in the fact that the Task Sequence fails.
After doing a lot of testing with a lot of help from a new colleague of mine Johan which did a lot of testing (not the Johan you think of;-) ) the value should be entered in Milliseconds instead of Seconds! Combining this value with the following two solved all our issues with applications not installing during the Task Sequence:
Today a hotfix was released as well, KB3007095, Applications may not be downloaded in System Center 2012 R2 Configuration Manager
To answer the question can you use Applications in a Task Sequence? Yes you can, works great when you have solved the above issue. Technet will be updated with this information as well and hopefully the hotfix will make it more stable as well.
I hope this can save time for someone.