[Verizon Galaxy S 5 Android Development] Maphack:
Wow, this is probably incredibly incoherent and I kept trailing off; taking a break from writing my essay and can't really think about using proper english atm. Hope at least something is informative or helps.

tl;dr tl;dr

If you're reverting to stock for the sole purpose of receiving OTA updates (I asked because this is what it sounds like you were doing), use Odin to flash firmware or modems instead.

Dirty flash when upgrading a rom to a newer version, saves a lot of time since restoring data/apps is not required.

Clean flash is necessary if going from stock to a rom or flashing a new ROM (factory reset: wipe data, cache, dalvik). Some people prefer to clean flash instead of dirty flashing because it might run smoother or something, but I don't recall having a problem.

tl;dr

Odin is nice because you can flash modems and firmware that you cannot do in recoveries. The method I almost used was the steps you took, revert to stock (which I don't even think I could without Odin) and take the OTA, reroot, and flash again. That process is pretty ridiculous and time consuming, which is why I inquired about your methods in the first place. AFAIK reverting to stock is only really necessary if you really want to get the newest version of android (however, people who did this on the S3 a while back had their bootloaders locked, so I prefer waiting), need to return the phone to verizon, or if you softbricked and need to odin back and start all over.

Clean flashes require a factory reset (data, cache, dalvik and sometimes /system, but I wouldn't format /system unless it is specified or I messed up somewhere and it's my last ditch effort before having to revert back to stock because I am unable to flash anything in recovery). Clean flashes are required when flashing any rom from stock or changing roms (which every thread already instructs)

Dirty flashes only require wiping the cache and dalvik. This is for flashing a newer version of a rom over an older version. Sometimes if I start getting errors because of some ill-advised tweak dirty flashing usually fixes the problem and saves a lot of time, so it can be useful in such situations as well.

I am kinda new; I just got Odin working for the first time a few days ago using parallels and it's been such a useful tool. I digress.

The unnecessary parts I was referring to was basically returning to stock. After flashing a rom on any device I had (I think Droid X was the first device I rooted, but I had an Eris) I never reverted back to stock unless something went terribly wrong (I think I screwed up my S3 a few times now that I think about it).

A lot of people like to clean flash. This requires doing a factory reset, data wipe, cache, dalvik, before flashing a ROM (possibly also formatting /system, but likely not a necessity). This is actually necessary if going from stock to any ROM or flashing any ROM over a different ROM. However, if you are only flashing a newer version of a ROM, unless stated otherwise, wiping only the cache and dalvik before flashing is necessary.

Using Odin you can sideload files through adb that cannot be flashed through recovery, such as modems and firmware in the case of the S5 (an educated guess is because of the locked bootloader, since I remember flashing modems on my S3). This is nice because modems do not require wipes and, as far as I know, won't mess up your phone.

Side note: I flashed this build without flashing the NE9 software and it seemed to run decently enough (I thought that if I flashed the ROM the program and method I was attempting to use without any success to flash modems/firmware would magically work). I didn't run it for very long before I nandroided back, though.