It's a bad example, but the principle still applies. All the things you're talking about doing are also painful, in the sense of what the article is getting at. Designing a system where you don't have to merge as often? Sucks. Figuring out your schedule weeks or months in advance instead of just doing it? Sucks.
These are painful things that you have to do, and have to get better at, and by doing them early and pushing through the pain, you avoid the real pain, the dangerous pain later on.
You don't need to plan weeks or months in advance. All you need to do is push that particular story onto the backlog and wait for a more opportune time.
There will always be files in a project that are more conflict prone than others, so it makes sense to be mindful of that when working on features in parallel. Perhaps it would even make sense to split the file to minimize further conflicts.
Pushing through pain that can't be avoided is fine. Pushing through pain that could be avoided with a little strategic planning is silly and wasteful.
What I'm seeing in this admonition is "when you feel pain, push through it now to avoid more pain later" instead of "when you feel pain, look for a strategy to reduce total pain over time".
And what I read was "quit procrastinating just because something makes you uncomfortable."
All the strategies you've described require you to face the problem head on and make an informed judgment about it, instead of just keeping on doing whatever you were doing. They're better strategies than the example that the article came up with, but they still require you to think about something that you've been avoiding.
These are painful things that you have to do, and have to get better at, and by doing them early and pushing through the pain, you avoid the real pain, the dangerous pain later on.