An intended workflow for videography with animation

First - You should never export MP4 video for use as a production master. MP4 video is comprised of I frames - which contain highly compressed color and luminance data that represents a compressed version of the original pixels for that frame and the compression is pretty good, and the color compression is not so destructive that you notice much degradation if you just go down one generation. The problem comes with the P (predicted forward) and the B (bidirectional predicted) frames. Everything about those frames is a mathematical calculation of both luminance and color information. It kind of blows my mind that it works at all.  If you use MP4's as your DI the best you can hope for is that 1 out of 4 frames contains a compressed version of the original pixels in the comp. I don't know any production house that would ever use an MP4 as a digital intermediate. You should use a visually lossless frame-based format for all of your Visual Effects and animation work. I use Cineform for a lot of my work because it is 10-bit, supports Alpha Channels, and the file size is reasonable. 

Now let's talk about sharing projects and efficient workflows. 

First and foremost - you must establish a directory structure and file naming bible that you follow all the time. I've been using the same format for 50 years. It started with my first job, writing shot names with a felt pen on the leaders of the thousands of spools of film we had to keep track of for the documentaries I was working on. This goes right down to the cut versions and the comp names in AE and the sequence names in Premiere Pro. 

Now let's talk file sharing. If you are a small shop the easiest and least expensive way to keep everything in order is a dropbox account. Here's the typical folder structure if I was starting a project for a client named "Mr. Big's Hat Shop" and the film was called "Johnny Nickel."

Dropbox/20-0626 MBHS Johnny Nickel

The numbers are today's date, MBHS is the client identifier, and Johnny Nickel is the Project name

Footage from the shoot would be stored in a Footage Folder in this file. Footage from each shoot date would be in a separate folder that started with F (for footage), then the date, then MGHS Johnny Nickel. There would be separate folders for Audio, Graphics, Scripts, and notes, Premiere Pro, and AE. Last of all there would be a separate folder for the edits and the MP4's that I would share with the client for approval. Only the RR 20-0626 MBHS Jhonny Nickel folder would be shared with the client but the root folder 20-0626 MBSH Johnny Nickel would be shared with my collaborators. If I had somebody out of the office doing music I would share the music folder and maybe the RR (test renders) with the composer.

That takes care of having access to everything on different systems. If the editor has a bunch of footage that nobody else needs then a separate folder with the unused footage would be stored on a local drive and then archived. I do this with most of my clients. Collaborators are not allowed to delete files, only to add them. When the project is complete then the Root folder is removed from Dropbox and stored on my backups.

That takes care of file sharing and project sharing. Let me talk about the workflow between AE and Premiere Pro. First, I try and never put more than one shot from a sequence in an AE comp. I don't edit sequences in AE unless there is no other way to transition between shots. Almost all of my AE work consists of very complex animations or visual effects and almost all of those shots come from a Premiere Pro sequence. I select, or I have the editor select the shot that needs work in AE and Create a Comp from Selected. The shot I'm working on in Premiere Pro has already been named appropriately. The comp that is created and the AEP is stored in the After Effects folder. As soon as the comp is created and the AEP is saved, we return to Premiere Pro, Undo the action to put the original footage back in the sequence, then change the color of that clip so it is easily identified as a shot that will be replaced with the VFX shot I rendered in AE.  I hope you followed that.

I almost always use Render Garder to create my DI (names appropriately something like this MBHS JNYN Scene 3 - 14 v1) which is saved in the VFX folder for the project and simultaneously render the Scene 3 shot 14 v1 MP4 for the client to review. 

I hope this helps a bit. Everyone that is involved in the project has access to the files they need any time because of Dropbox, the critical files are archived in the cloud, and as soon as the project is wrapped, the root folder is moved to the archives and dropbox space is freed up again.