The problem is while Affinity Designer may recognize the layers, your printer or a client's printer is more likely to be using an Adobe product. The compatibility issue is quite critical. I would love to use Designer and Affinity Publisher as alternatives to Adobe's CC but that isn't possible in most cases without restructuring documents in Illustrator. The PDFs provided have a single layer with nested layers - in Adobe language that is a group and they would still require restructuring for
Until Affinity makes this a tool that can be used in professional projects, Illustrator still needs to be the go to application since Freehand was killed. However, for the moment QuarkXpress is quickly surpassing Indesign in version 8 and the upcoming version 9. It's not cheap but you own it....