1. I think if one knows he has even a thin layer of rust in the bottom of the tank, it is "always" best to flush out the tank "prior" to installing the in-tank filter.
2. After the tank is flushed out and the bottom is clean of loose rust particles, sand, or other debris, any subsequent "heavier than gas" rust particles that occur in the tank with remain on the bottom just like the "heavier than gas" rust particles stay in the bottom of the sediment bowl ..... they will not float.
3. If an in tank filter was installed in a "clean" tank, and if this filter gets clogged while on the road, say a few years afterwards, this is usually a good sign that one is:
a. Usually almost out of gas; and,
b. Has a small amount of crud sitting way down on the bottom of his tank; and,
c. The upper part of the in-tank filter is exposed to the air as opposed to being exposed to liquid fuel.
d. Just add gas so the top of the filter will be surrounded by gas and be on your way.
Then further down below for a comparison, there is a carburetor gas strainer screen that is different.
It can fill up with crud and get clogged because the heavier than gas rust and crud cannot fall out or fall off from the screen like that of a vertical in-tank screen.
I have an in-tank for six years working great ..... I wish I could live to see enough rust in my rusty tank to witness it getting clogged.
Appears if the total surface and length of an in-tank filter screen gets clogged just after a few years of service, this is not at all normal, and one would need to find what is clogging it.
And finally, if a full tank of gas cannot be removed through the bottom of the tank for any reason, it would have to be siphoned through the top opening.
I do this too sometimes ..... easy .... drive about 10 miles to get a full tank of gas in my van, return, and rather than fool around with gas cans, just siphon it into my lawn mower.
Hope this helps.