Use a swatch like CMYK 0,0,0,100 or CMYK 0,0,0,90 or CMYK 100,0,0,0 for a column rule and turn on overprint.

Overprint attribute will not applied to the column rules.

Tested with InDesign 17.1.0.50 on Windows 10.

For more details see into this discussion at the InDesign User Forum:

column line do not overprint
davidl72327298, 28.03.2022
https://community.adobe.com/t5/indesign-discussions/column-line-do-not-overprint/td-p/12843115

Download a sample document from my Dropbox account:
https://www.dropbox.com/s/ug0y2uvhetdlwdh/ColumnRules-DOES-NOT-Overprint.indd?dl=1

Below the links to two screenshots.
One is showing Separation Preview with all inks, the other one Separation Preview without Cyan; and this one is showing that CMYK 100,0,0,0 does NOT overprint the yellow background.

https://www.dropbox.com/s/sc7jn63l8tdt8gk/ColumnRule-Overprint-BUG-CustomSwatch-1.PNG?dl=1

https://www.dropbox.com/s/pb3up4o0ivrl3kv/ColumnRule-Overprint-BUG-CustomSwatch-2.PNG?dl=1

NOTE: It seems that ONLY [Black] will overprint.
Or all tints of [Black] as long as the tints are applied to the column rule in the text frame options dialog for column rules.

Also tested color "Cyan" by scripting. But also this color will not overprint.
See page 5 in my sample test document.

Regards,
Uwe Laubender
( ACP )