The stock frames flex and bend. I have seen a lot of broken cases that show signs of touching the swingarm but they often had over 1/16" of clearance between the cases and swingarm when you inspected them. The majority of the bikes that showed signs of contact between the cases and swingarms were race bikes that really got pounded on the track, fat guys that did a lot of jumping or the bike had insufficient suspension for the abuse the bike was taking.
The 250R frame has basically an isosceles trapezoidal shape. 4 sided structures are not very resistant to collapsing when loaded from any side if they do not have triangulation from one corner diagonally to the opposite corner of the trapezoid. The head stay used the engine to add some very crude triangulation. The head stays were always breaking indicating they were trying to prevent the 4 sided structure from collapsing. Not running the head stay allows the frame to bend and flex (collapse) allowing the swingarm to move closer to the cases.
Many guys removed the head stay to prevent the head gasket from leaking and or breaking the head stay or breaking the head stay tab off of the head. This was just another indication the frame was flexing and head stay was trying to prevent this from happening.