I don't find this to be true once you have automated production of all the buildings and use construction bots. Combined with the recent(ish) improvements to blueprints, blueprint books, and cut/copy/paste makes fixing those off-by-one errors quite painless: 1. Ctrl+X to cut and auto-deconstruct the build, 2. Ctrl+V to paste in the correct place, 3. Go fix something else for 2 minutes. :)
It's possible they didn't reach construction robots yet. The game becomes more interesting once they allow you to refactor with ease.
But I don't particularly like the comparison because a huge thing about Factorio is the restrictions on physical layout. Due to this physicality it is very expensive to refactor in Factorio, you are going to be working with more components working together at the same time, and the fine details matter way more on every level because if you're off by a single tile, it all comes crumbling down.
Because of this, in Factorio you really cannot refactor your way to a base producing something at a new rate in Factorio. The only method is to design a brand new production line from scratch and rebuild - basically, all you have is waterfall and rewrites in your toolkit.