your not gaining the full value from the color in your video. You loose White Balance and other qualities from your vector scope from using raw files instead of transcoding them.
Never encountered more unprofessional, false and misleading comment on this Forum. Start here, then you'll probably understand why.
Always and i mean ALWAYS transcode your footage off the chip.
Never, and I mean NEVER, transcode your source footages for the sake of transcoding. Transcoding may help if your machine is underpowered or you're going to do a compositing work and, hence, more power is required to decode several highly compressed footages on the fly.
Do your self a favor, take a raw .mts file and a pro res 422 file side by side in scope and look at the difference.
Do yourself a favour, transcode a source footage into any 4:4:4 production codec, import both footages into After Effects, set project to 32-bit and linearise working space for higher precision while blending. Drop source and transcoded footages into the same composition and set Blending Mode to Difference. If there are some super-whites in the source footage, they will be clipped, and you'l see some artefacts there. If not, you'll see an almost pure black solid, which means there is no mathematical difference in pixels values.
With 4:2:2 transcoding you'll see more artefacts, which means you get less precise data in your intermediate.
Is it sufficient to save the "STREAM" folder in order to have all the necessary meta data or do I need any of the other folders/files?
No, metadata are not contained in the STREAM folder. Copying the STREAM folder only may be sufficient for editing short AVCHD clips, but for spanned AVCHD clips you have to copy the entire folders structure on your HDD.
Will Premiere be able to differentiate between the files with same names? What is the best way to keep an order within my project (window)?
You need to properly organise files on your HDD as well as imported clips inside PrPro project. You can create e.g. CAMERA_1_SCENE_01, CAMERA_1_SCENE_02 folders on your HDD and respective bins in PrPro project.