Re: "Can you run 3/4" FLEX thru a wireway to isolate emg. power" -- sounds fine to me.
Re: "and not use a connector when entering and exiting a indoor wireway" -- what connector? where? A flex-wireway connector? Yes, you'd need to provide a nipple, j-box, or similar where the flex passes through the wireway wall.
Code references: well, the installation you're describing is somewhat unusual, so there may not be any specific code references, but here's a couple that come close: 300.12 and 314.17(A). I suspect any inspector would say those two paragraphs justify the requirement for you to provide a nipple or similar where you enter the wireway. And keep in mind that the inspector could require you to do so just because he felt like it, even if there was no code requirement backing him up.
And as cheap as two nipples or j-boxes are, why fight it?