This is a bit of a re-imagining of https://www.thingiverse.com/thing:1610834 --- thanks for the inspiration!
My main need was for M2 holes instead of M3, and I also wanted to offset the M2 portion so I could bolt it together properly.
Print it, stick your M2 bolts pointing upwards and attach your stack as normal as if it were the bottom of the frame. Put the whole thing on the frame and screw your M3 bolts upwards, secure with a nut.
The total height is 4mm, where the M2 section is 2mm. You can just squeeze in a socket cap M2 screw.
I've made a newer version with thinner walls, enough to get out of the way of your board so you don't need lower standoffs. There are also half and quarter versions if you find you are in the way of your battery strap holes or similar.
I printed it (M2 holes against the bed) with support. The opposite might work better for you.