As Michael says if something works for you then stick with it but it might be worth you watching the Tutorial Rebacca linked to covering the asymmetrical dowel hole method, from your post with the illustration it looks like you may be doing something wrong which could give the misalignment in the dowel locations.
There is nothing mirrored with the latest versions of the software by the user as there may have been with earlier versions of the software, create your artwork on one side of the material select what needs to go on the other side & then using the right click menu select copy to other side, the software handles the mirroring & placement of the selected artwork so both sides align properly.
When you come to machine the job you only set your x y zero position once. Position your material, clamp, set your x y z zeros, machine first side. Move gantry out of the way, machine holes for dowels in spoilboard DO NOT touch your x y zero move gantry out of the way if needed to & replace your material for cutting the other side. Again do not alter your x y zero even if you have to do a tool change & reset your z zero. Machine second side, remove from machine & feel proud of yourself for perfect alignment
More than one way to do lots of different jobs so stick to what works best for yourself