like the others have said, layering is best on the intended surface.
Nobody here addressed the *why* you're getting the bubbles; It's because of the layered vinyl is higher at the edges than the layer below it.
Your squeegee cannot make full surface contact because of this gap - as small as it is. In your photo, you have some larger bubbles that are farther away from the layered edges, which to me looks like not enough pressure being applied during installation.
Yes, you will always get tiny bubbles around the edges of layered vinyl when installed.
We only pop the largest (1/8" or larger). The smaller bubbles go away after a few days on their own.
While it is best to install in layers, it's not always possible - depending on the surface you're applying to.
We install 48" wide x 24" tall pre-assembled two-color layered logos (dry) on semi trailers for best results.
We found that going over rivets or sometimes corrugated surfaces plus rivets and seams is much easier to do when pre-assembled, not only for alignment purposes, it also saves time from working around said rivets twice for each graphic. We'd love to be able to print a one layer logo for this company, but the main color is gold metallic which makes that impossible.
When possible, we do install in layers for best results.