Yes, that's how it works. You lose the manufacturing output for the rush buy turn, be it a ship or structure.
To compensate, I only rush buy a factory or two in the beginning and then let the factories build whatever. Sometimes, during that turn, I'll adjust the output wheel to 100% econ or research and move it back after the rush buy. I'll rush buy the Hyperion Shrinker if the planet it's on doesn't have a built up factory base, but that's about it.
As far as ships, I only rush buy a few of them in the beginning as well. If I'm in desperate need of a ship later, I'll rush buy one, but that's pretty rare. The BCs can go to buying techs and upgrading ships instead. I don't bother with the slider in those cases, but would be more efficient if I did. The problem there is that I'd need to adjust 5 sliders back and forth.