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There are only two correct choices:

1 – put it in the surname prefix
2 – Manually create the NAME record and put it in there.

As for the married name, you have to remember that the _MARR _MARNM that we use is a non-standard GEDCOM tag, so it is what it is and no more than that. If you want to use it (as I do) then you can let the system auto-create it for you. If you put the surname prefix in the husband’s name, then (for patrilineal naming conventions) the surname IS included in the wife’s married name.
Alternatively you can also manually create the married name (click the edit button beside the auto-created version).

The alternative to _MARR _MARNM (which I see webtrees are planning to remove: https://github.com/fisharebest/webtrees/issues/794) is to add multiple names.

1 NAME John /de Bourbon/
1 NAME John Bourbon

The solution to wanting multiple surnames (de Bourbon, and Bourbon) is to manually create the NAME and put the alternate in the SURN field.

1 NAME John /de Bourbon/
2 GIVN John
2 SURN Bourbon, Burbon

For sorting purposes surname prefixes are generally ignored.

Outside of these, I can only strongly recommend you don’t try to create new solutions outside of both GEDCOM and the kiwitrees coding conventions. They won’t work well, and are likely to break if code is changed (as it constantly is).

Nigel
My personal kiwitrees site is www.our-families.info