Rule of thumb is the boot drive is where your apps will live. So you are correct if you’ve setup your external as the boot drive then you do want to hod the apps on it.
Thats not to say you can’t run some off a different drive! But, it depends on the given apps needs.
Some Apps allow you to alter their cache & scratch space either via a menu option or having to go into the apps settings with an editor. Adobe Flash Player sadly needs to be in the boot drive and frankly you want it under the higher security level of the apps folder.
The word ‘Data’ can throw you as that could be anything! To add to it there is a lot of mis-information on how to effectively setup drives in general.
So let’s start at ground Zero! Lets say you have a brand new system and you run it on for the very first time. Apple has already install the Os and the setup screen will prompt you for the needed first users info. This is where I take a left turn! This first user is defined as the systems Admin! So a good habit is to set this user up as a user account to manage your system not user it (make sure to make a strong password and write it down somewhere safe)! For installing apps and OS updates. I generally don’t use my name but something that I can remember is an admin account. Once this account is made I go into the '''User & Groups''' control panel account to create my daily user account. This account is setup as a ‘Standard’ User and I still want a good password for this account but one I will remember!
OK so installing apps using the Admin account and using the standard account for my day to day stuff setting up my email account and other settings for the apps here.
Now lets talk about Apps & Data segregation! Ideally, if you are a heavy data person you what to use either a separate partition if you have a very large drive or use a separate drive for your data isolating it from your apps. This then gets into using the faster I/O for your OS and Apps drive, and using the slower as your data drive.
If you have a 27” iMac you have two I/O’s available a fast PCIe/NVMe interface and a slower SATA III (6.0 Gb/s) interface. If you have a 21.5” model you may not have the faster PCIe/NVMe interface as Apple only installed the needed parts on the SSD only or Fusion Drive’d systems to support it and there is no means to add it later.
If I remember correctly you were getting a 21.5” Fusion Drive model and wanted to know if you could add in a blade SSD. I think I had recommend you just use the system as is and use an external drive as a backup. Which I would still do here. And once you have some coin get the larger OWC Aura drive making your system a true dual drive setup with the Aura PCIe/NVMe blade drive be your boot drive with the apps and leaving at least 1/4 free for the OS to leverage.
Using an external drive as an OS/App’s drive can be dicy! As if you break the connection your system can freeze up if you knock it.
Thats why I do recommend dual partition or drive and not an external