We will take a look and see if there is some way to respect the specific distance between tools you like to use for tool placement. There must be a hard coded value somewhere that specifies how long those lines should be between tools.
I agree that can be really annoying. I space my workflows pretty tight as well and I plug in a new tool and have to realign every downstream tool. Great suggestion!
Designer auto adjusts when you drag a tool between tools. Also, check out selecting multiple tools and use the distribute evenly functionality. I hope this resolves this issue.