That clarifies things a little, I think.
4000 PSI burst discs are used in low pressure steels (3AA-2450). These cylinders have a hydro test pressure of 4083 PSI (2450 * 5/3). A fill to 3500 would have been 85% of hydro test pressure and 87% of the rating of the burst disc. Burst discs have a tolerance of +0% and -10%. Put another way, they are supposed to release somewhere between 90% and 100% of their rated pressure. It is not hard to believe that repeated fills to 87% of rated pressure could cause a burst disc to rupture.
I get air at 3 places depending on circumstances, and none of them will fill a cylinder in excess of its rated capacity, though they will sometimes fill a + stamped cylinder to 10% over. If a cylinder is hot from filling they will wait for it to cool and top it off, but they will not fill it to a higher pressure in anticipation of the pressure dropping as the cylinder cools, even though this is an approved practice. None of these places have fill stations that are separated from customer areas. None of them secure cylinders before filling.
Whether burst discs provide added safety on scuba cylinders is a difficult question. In a fire, typically the walls of the cylinder will fail before the burst disc does. As pointed out upthread, burst discs aren't used -- indeed, aren't allowed -- in Europe. But from what I understand they don't practice "cave fills" there, either, and there are mechanical safety controls in place to prevent overfilling a cylinder, accidentally or otherwise.