Infraviolet:
To clarify, are ISP programmers for bootloading and USB-TTL FTDI adapters for programming typically the same device or not?
The short answer is they are different tools used for different purposes. The long answer is that it actually is possible to use an FTDI FT232 as an ISP programmer but it's super slow and there is no support for doing so via the Arduino IDE. I've never heard of someone actually doing it, other than an article on adafruit.com. The only occasion where I would consider doing that is if I needed an ISP programmer and only had an FTDI. But that would be rare in the Arduino world since we can make a spare Arduino board into an Arduino as ISP programmer, which is easier and superior to the FTDI as ISP option.
Infraviolet:
I tend to use a Linux OS rather than windows, so would my situation be the same when you mention drivers attempting to brick FTDI devices?
I'm pretty sure that situation was always limited to Windows and I think FTDI even stopped doing the bricking thing. I switched to an alternative driver after that happened so I don't know what the situation is.
Infraviolet:
When using such device(s?) do I just run the arduino IDE as normal and use it for programming as normal, except that a specialised little USB will be used for bootloading or programming the ATMEGA chip, or must other settings changes be made?
To upload using your FTDI or CH340 adapter you only need to select its port from the Arduino IDE's Tools > Port menu. No special settings are needed.