The 3dsmax QT support is deeply integrated into the 3dsmax submitter, so unfortunately there is no easy way to port that code to the AE and Nuke submitters. The least invasive way to do what you’re looking for in Deadline 4.1 is to write a generic post job script that grabs the output information from the job that just rendered and then submit a QT job to make a movie from that output. You would place this script on the network somewhere, and then edit the Nuke and AE submitters to add the following line to the job info file they create (this is the file that defines the frame range, priority, pool, plugin, etc):
PostJobScript=\\path\to\qt\script.py
Now we don’t have a pre-written post job script to do this, but one can be pieced together using the post job script example here:
thinkboxsoftware.com/deadlin … ob_Scripts
…and the QT event plugin script I referred to earlier. The Post Job Script example shows how to get the output file paths, and the QT event plugin shows how to submit a QT job to Deadline once you have those paths.
I don’t have any experience with AE’s watch folder system, so I took a look at the documentation:
help.adobe.com/en_US/aftereffect … 79a2a.html
From what I’ve read, it seems like a pretty bare-bones system. There likely isn’t any difference in terms of rendering speed (both systems use multiple machines to work render frames from sequences simultaneously), but there are definitely benefits to using Deadline from an artist’s perspective:
- The submission interface seems more elegant, and allows you to control additional options like memory management and multiprocess rendering.
- Monitor application allows one to control and modify jobs after they have been submitted.
- Render logs and error reports are easily accessible from the Monitor UI.
- Deadline can notify you via email when you job is complete or when it has failed (so you don’t have to keep refreshing a web page).
There are many other benefits as well (priority systems, having all render jobs controlled by one render manager, etc), but I tried to focus on the Artist experience. ** Note that I’m making an assumption that the watch folder system doesn’t have these features, and I’m basing that assumption on the documentation I linked to above.
In the Deadline submitter, there is an option called Concurrent Tasks. You can increase this number to 8, and then each node will render up to 8 tasks at a time (using 8 instances of AE). By default, a node will only dequeue as many tasks as it has CPUs, so if you set it to 8, you don’t have to worry about your 4 core machines picking up more than 4 tasks.
As far as I know, AE renders a frame using a single processor. If you enable multiprocessing, it only works if you are telling AE to render a group of frames, as AE will use one processor per frame. So as long as the node has the RAM, there is a benefit to using concurrent tasks in Deadline. Just make sure to disable multiprocess rendering when you do. 
Hope I’ve been helpful!