I guess it's due to weight of the heatsink and because I can only use six out of nine stand offs, since it's a mATX board inside an ATX case. Is this dangerous? I mean it's barely noticeable and it runs fine, there's only like a 1mm difference. Actually I have an idea, what if I insert the rest three stand off upside down, so they'll be fixed inside motherboard holes while not needing any case holes? I mean, they'll still support it, right?
Do not see this as dangerous. As long as the mobo is working and everything works, then should be no issues.
I suggest adding in the last 3 stand-offs and placing washers/spacers between the mobo and the stand-offs to make up the 1mm space.
Another idea is to install all 9 standoffs and screw down the 3 in question first, then follow up with screwing in the remaining 6. Be sure to only thread the screws to start, do not tighten all the way, and screw them in a criss-cross pattern. By only threading all the screws, and tightening in a criss-cross pattern, it will ensure that the board will align itself with the standoffs and seat properly; it may even take the bend out when all screws are fully tightened.
I do not recommend turning the stand-offs upside down as they will only support the weight of the mobo if it is in a horizontal position; as soon as the mobo goes vertical then the upside down stand-offs do nothing.