"Ain't bothering me" as an attitude applies if you don't have an attachment to the person. In this case, the partner is actually bothered by it. They don't have a right to force a halt but concerns about major behavioral changes are reasonable for a loved one to have in this situation. "Ain't bothering me" also only applies if you disregard the potential damage to local underground infrastructure, other people's property, hitting a gas line and cause a major issue, etc.
If they're in a rural area where those aren't potential issues and the boyfriend doesn't want to change, then the partner simply has to decide if they can live with the new situation. I think we'd agree on that.
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I'm confused on your comments about reading into the partner's mental health. I see no indication in their post saying they're concerned about how it looks to others. As for non-conforming, they seem to be somewhat accepting, stating that they haven't made it a big issue before because the boyfriend seems relatively happy. They specifically say, "My biggest concern is his safety". That seems reasonable. Major behavioral changes on the other hand would be a bigger warning sign. (while acknowledging that a red flag doesn't mean there's an actual issue)
EDIT: From an update [1] here's why the boyfriend says he does it: "It’s just pleasant. When I’m down there, I feel safe and calm, and I’m always happier when I leave than when I went in"
I suppose there are worse coping mechanisms than that.
[1] https://www.reddit.com/r/BestofRedditorUpdates/comments/u6a3...