What OS are you using?
All I want to do is make the first possibly second iteration of the new iMacs so if I run a SSD as boot and day to day running via the USB, will it function as per it is now with the fusion and still run at a similar rate?
Maybe it is because I am going to sleep soon, and pretty tired, but I read this multiple times and I cannot understand what you are asking.
Are you saying that you are trying to use some type of external storage solution for your Late 2013 iMac to keep your iMac going until the M1 iMacs are out sometimes in the next few years?
And, your only concern is whether or an external storage solution would be as fast as your existing Fusion Drive?
I have ran all sorts of external drive as boot drives. FW400, FW800, USB2, USB3, TB1/2, TB3, thumb drives, SD cards, PATA, SATA, NVMe, External HW Striping RAIDs, External SW Striping RAIDs, etc..... I have even ran MacOS on old iPods.
There is nothing wrong with running MacOS on an external drive, and cannot ever remember having an issue with it.
Getting a SATA SSD and a USB Enclosure or USB3/SATA adapter cable is really affordable now. A 1TB SSD and enclosure could be purchased for less than $90 if you are in the US.
Speed wise, you would probably see similar speeds to your Fusion Drive. USB3 will give you about 400MBps speeds. Your Fusion Drive when it was brand new would most likely beat this speed unless you were doing long writes or if you were accessing data that was stored in the HDD.
The SSD portion of a seven year old Fusion Drive would probably be slower than what you can get with a USB3 SSD.
and still run at a similar rate?
I have booted my Late 2012 iMac from USB, TB1, and TB3 drives (connected to the TB1 port). My iMac is currently booting from a Samsung X5 NVMe TB3 drive via the TB1 port, and gets speeds almost 900MBps.
There was no real difference in speed when booting from SATA USB and SATA TB1 drive. I get about 350-400MBps with both.
I didn't try it, but someone on the forum with a Late 2012 iMac booted from a TB2 NVMe drive, and got speeds about 700Mbps via TB1.
Is there any point thinking of using the thunderbolt port?
The biggest downside to using USB over Thunderbolt is the lack of TRIM support for MacOS with USB drives.
TB drives have TRIM support.
I personally suggest just going with a SATA USB3 enclosure or adapter and a SATA SSD.
This will give you decent speeds compared to your aging Fusion Drive, but will not cost that much. You will not have TRIM support, but if you plan on getting a new iMac in the next few years, this won't really matter much in the long run.
You could see a decent speed increase and TRIM support if you go with a NVMe SSD over TB2 or TB3, but this would cost 3x as much per GB as using the USB3 solution (400MBps).
You could spend more than twice as much and get a TB2 NVM SSD (700MBps) as a happy medium between speed, TRIM support, and cost.
If speed was your goal, you could go with a TB3 NVMe (900MBps), but you would also have to get a TB3 dock to power the external TB3 drive, an Apple TB2/TB3 bidirectional adapter, and a TB2 cable. So, probably a bigger investment you were planning on making. The silver lining is that you could continue to make use of the investment on your next iMac, but run the NVMe at full speed (3000MBps).