As Vans have developed the line of products, the build instructions have also developed. Still a way to go, but much more comprehensive than say a 7 or 8, which reflects what the 12 is about. Shake the box, assemble the contents, fly.
There are a lot of reasons to build in order, to stay on plan and do things their way, mainly because the LSA design has been optimised to keep weight down. For example, there are a lot of through structure fasteners in the fuselage which require other sub items further down the line to be completed before finish riveting.
For that reason alone, I would stay on track with their sequence.
Make sure you know what options you have - cross reference how electrical options interface with basic wiring and flag pages to ensure you don't move too far forward and have to undo stuff. That is important for avionics as we found out. Once you decide which option, download the relevant pages and mark up as you go into fuselage wiring - lots of gotchas.
The wings are easy but have electric options and yes, the lighting takes some thought, especially as they have asymmetric plugging on the wing wiring - get a good magnifying glass and a 10x lupe
Top tip - pay attention and make the bending jibbler accurately to do the tips - they are a breeze then and don't worry about the degrees, it is a bit.. a bit.. a bit more.. a bit more.. a bit less.. etc.
Once the emp and wings/flaperons are done, they can go away which gives you loads more room in the shop. We are building 2 kits simultaneously, so our woes are doubled. Mistakes are only on airframe #1 though
As others have said, there is a lot more work in the fuse and once you are close to finishing it, you don't want to look at the wings and say - I wish they were ready, I can sit in my aeroplane now, but I can't fly yet
I hope that the introduction of the 12iS will bring about a complete refresh of the build instructions - they need it badly because the 12 has been around for a bit now, but as they are, they are still good provided you read, read and read again.