Great question, @seewhy!
Am I understanding this right: You are using Entities already and you have a Dataset (which we're starting to call Entity Lists). This entity list is missing a column of data, and it would be really useful if you could add that new column and populate it with data (which you have elsewhere, like in other submissions), and you're comfortable doing that via the API.
If that's the case, I think your approach sounds good. I have some small hacky suggestions, such as if you need to add another property to an entity and you don't want to make a new version of your form that gets sent out to everyone, you could make a separate form that adds the new entity property and doesn't get distributed, and then you would be able to use the API to update/fill in that new property in any existing entity.
I might be misunderstanding your situation though! (I think my main issue is not being clear on whether or to what degree entities are already involved, and also being curious but not super well-informed about how geodata gets managed in systems outside of ODK such as QGIS. I'd really like to understand, though!)
It also kind of sounds like being able to view and edit traces is important, and that's something we couldn't really do yet with entities (w/o making external API calls like you're talking about) but are actively working on. @LN just made this post outlining some design decisions about updating entities via submissions: Update an Entity from a form submission with server-side conflict detection and resolution