Bypassing stuff of other mods makes a mod pack fun, if I wanted to play each mod individually I would. If an author doesn't like that he/she has 2 options, 1) don't allow his/her mod to be used in packs (Better than Wolves?) or 2) Improve the aspects people avoid to the point people like them more than the alternatives.
But I don't think mod creators really care (at least not of the mods in FTB), I mean if they would then why give us all these ways to convert power? I mean Forestry cuts itself by adding an engine that converts IC2 Solar Power into BC MJ power. If Sengir really would mind that than he probably wouldn't have added that engine.
Also, Forestry, Railcraft and Thermal Expansion are (originally) BC add-ons, they are supposed to give alternatives to the regular BC stuff and if the author of BC really had an issue with those add-ons he wouldn't have created BC to be as open as it is for modding (as far as I know BC is designed to allow people to add their own stuff quite easily, if the author has a problem with that he wouldn't have designed it that way). And most of those add-ons add ways to generate IC2 power as well, because IC2 (just like BC) is a quite open mod that allows things to be add onto it.