For complete clarity on previous warnings.One of the RC/TE issues can be solved by holding conduits in inventory and not in world while updating. Another issue, the one that corrupts worlds, can only be solved by updating TE3 to 11b or higher. The second issue so far tends to be only in worlds where RC's hidden block, Factorization's Wrath Lamps and or TC4's Arcane Lamps are present. This is caused by a vanilla bug involving "invisible/hidden" blocks interacting oddly with TE conduits and ducts. The reason it only shows up if RC,TC4 and/or Factorization are installed with TE is because those seem to be the only mods using the flawed vanilla code relating to "invisible/hidden" blocks. The reason it is typically labeled as being a RC bug is because only RC spawns those blocks on its own with no player action required. The other 2 mods you can avoid the interaction by not using Arcane Lamps or Wrath Lamps. In 11b TE3 changed the way their blocks interact with the flawed vanilla code to ensure that even if another mod uses that code it won't cause the issue.
So :
TE didn't realize the vanilla code was flawed because they weren't using it
FZ and TC4 only use the flawed vanilla code if you place a specific block
RC uses the flawed vanilla code to track player movement. It spawns more and more of the blocks the more a player moves around and the more players there are. This causes more opportunities for the flawed blocks to interact with other modded blocks. Which is why many people report it as solely a RC issue.
Other mods have also been affected by the flawed vanilla code when RC is installed. TE just has the most obvious interaction. Current affected mods include MFR and Forestry as well as TE3.
Of course there is much more accurate coding language to describe this but for the average user it boils down to
Bugged vanilla code used by 3 mods interacting poorly with a fourth mod. Said fourth mod has fixed it on their side even though the flawed code is not used by their mod.
As of right now only RC is proven to be using the troublesome vanilla code. FZ and TC4 are suspected of it but do not seem to cause the issue as consistently as RC. Of course there may be other mods using it as well. We don't know and we can't exactly go looking through all the code to see if that specific vanilla code is being referenced. If a mod has "invisible" blocks (Tile Entities only). (Blocks that can only be seen with glasses etc )It may possibly have the issue. Interesting as "invisible" blocks may be they may or may not have cross mod issues due to the flawed vanilla code.
TLDR : Its not RC/FZ/TC4/TE3's fault. Its a vanilla flaw that was revealed when the mods interacted in a specific way.