Setup? Pull it out of the bag. Done.

Silt? Let's see... I've had to let the water settle for a while at times. I think if I were going anywhere where the water is full of silt and mud to the degree that a clog is a guarantee, I'd take a fold up bucket (I've seen people use a gallon milk jug with the top cut off, carried over the end of a sleeping pad, for a bucket) and add flocculant to settle out the sediments BEFORE filtering it, regardless of the type of filter I took. It would take as long as it has to take... but the water would be clean and drinkable at the end. I do not know of a backpacking filter that would not clog if you overwhelm it with water from the Colorado River at high flow or in desert mudholes... There are limits to everything.

There are degrees of silt - the Amigo Pro has a bit of tube in the bottom and when full the filter sits up off the bottom of the bag. So letting it sit for a while before starting to filter might help in some cases, but certainly not all. It's worked well with the little bit of sediment I've encountered.

Very late in season or when going anywhere I know there will be small puddles, I still take the Hiker Pro, which uses the same cartridge as the Amigo Pro. Most of the time I take the Amigo Pro. I definitely am not a desert person, too much heat turns me into a zombie, but I do go into low elevation parks at times that were formerly ranches, where water sources can be... iffy. If you are wanting something that will handle water that's beyond iffy, I don't know that any backpacking filter by itself would be up to the task. There has been water that I both filtered AND threw in Micropur and waited well over an hour before even trying to drink it.