The time finder used both for IV's and the PID. To clarify, if you want a shiny, you have to click the "nearby shiny frame" (even for gen 5) so that way you can find the appropriate seeds. So you would input all the relevant info (shininess/nature/iv's etc) into the time finder.In the guides you read they must have been very clear that in the Time Finder Window the min/max frame must be set to 1 (both) to simplify the RNG process since is kinda difficult to accurately advance the IVRNG. Also the time finder is ONLY to get a seed for a desired IV's spread (in your case a HP Fire spread), for any other info of the pokemon (nature, shininess, gender, ability, etc) you need to input the seed you found onto the RNG main window. I suggest you to re-check the guides you used and post any question on this thread.
About the "nearby shiny frames", i think you don't use it for 5th gen RNG, but don't quote me on this since i'm not sure. I always searched shininess on the main window.
Edit: To be clearer, you could just use the time finder to find the seeds for the Iv's that you want (which is what you are doing by choosing the IV (standard seed) method). By putting in the nature/etc that you want as well, the reporter limits the results to match your input so that you do not have to search all the valid seeds for your IV's in order to find one that has a reasonable shiny frame as well.
tl;dr. Putting in all of the info/stats you want in the time finder allows the reporter to do all of the search work for you, making it a lot easier to find what you want. So you want to check "nearby shiny frames" if you want a shiny
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