Thanks! The Help page you gave tells mostly that uncertain should be used on information from secondary sources. It is indeed not very helpful for this case.
In the catholic part of the Netherlands there is a distinction between 'doopnamen', which are often a Latin or biblical names, but it is used as official name, like on your passport and in government documentation, and a 'roepnaam', which is often a Dutch version of one doopnaam. The roepnaam is also used in a formal context, while the doopnamen are only used on some official documents. Maybe it's comparable with Bill Clinton, whose proper first name is William, but Bill is also used in a more formal context.
As far as I can see the Dutch convention here is to put the doopnaam/official first name in the proper first name field and the roepnaam in the preferred name field.
Adding the proper name by default in the preferred name field, would at least bring in some uncertainty, even though a primary source (the birth certificate) is used. So I think I'll follow you idea to mark it as uncertain.