Do all of the root methods leave you in the lurch when it comes to OTA updates?
Only if you modify your ROM, kernel, modem, recovery, or system applications. So ...
Flash a custom ROM - OTA update will fail
Flash a custom kernel - OTA update will fail
Flash custom recovery like CWM - OTA update will fail
Flash a different modem than the current official - OTA update will fail
Remove bloatware like Sprint ID - OTA update will (probably) fail
If you just root your phone, just to run Apps that require root for example, then OTA updates can be installed just fine (edit - how many times can I say "just" in the same sentence? geez!), but remove root in the process, requiring you to re-root if you choose to do so. If you do modify any of the above, flashing back to full stock in order to take an OTA update is quite easy using Odin so its mostly a non-issue. However, the full update is usually available to flash before the update even goes live, so it usually makes more sense to just flash that then go back to stock.
As has already been stated since your post, Android is as open as it gets. It's the device manufacturers and carriers that lock the system down, for a variety of reasons that all have to do with maximizing profits. Flashing phones = more warranty claims and service calls which cut into those profit margins. Samsung Android phones are actually a bit more "open" than say HTC or Motorola phones as Samsung does not lock down the bootloader. REAL exploits like Revolutionary S-Off and others normally overcome this issue, but this phone is technically a bit more open than others.
The current root method that is linked in this thread really does pass the caveman test.