Yes it matters, and one does not need to be a chess fanatic to know this. The rule is white is right, queens on their own colors, but it is actually much more universal than chess. Checkers uses the same board and the same white is right rule. Odds are quite good that this board arrangement started with the ancient game of draughts. If that is the case, then we are talking about thousands of years of precedent. But then detail incompetence has become a hallmark of many software so-called engineers.
From a gameplay perspective, it matters not. It may be unsettling and more error prone, but it matters as much as "you must wear white at wimbledon" to the theoretical state of the game.
As long as the board is setup symmetrically and the relative position of the other pieces is the same, neither the color of the righthand corner, nor whether the queen gets her own color matters (you still have a short side and a long side which will presumably be respected for castling).
Now there is some utility to the conventions - in that when a player looks at a game in progress they have a good idea how it got to that position partially based on knowing what the short/long side are at the start. It also allows two players to quickly setup their side of the board in a consistent manner to reach a symmetrical start. And the short-side always being on white's right and black's left allows algebraic notation to be consistent (it would need to be mirrored horizontally if the king/queen positions were).
But none of that is terribly important to a nonfunctional decorative chess set in a lousy browser game
