The manual syncing with the Finder or iTunes and the iCloud syncing are mutually exclusive. As soon as we enable iCloud Photos on a mobile device all manually synced photos will be erased. Turning on iCloud Photos is a quick and easy way of getting rid of all synced photos at once.
The synced photos are just a selection of photos and videos intended for viewing on the device. And they are delivered downsized, optimized for the iPhone or iPad, just large enough for the smaller displays.
The synced photos are kept separately, because they might be duplicates of photos already on the iPhone and because of the lesser quality.
When we want to have the photos in the full quality on or mobile devices, properly imported to the library, we need to transfer them differently, for example by Air Drop or Mail or with iCloud Photos.
The sort order of photos in synced albums has been a problem ever since Apple introduced the feature to sync albums with photos to our mobile devices, even in the good old times of iPhoto and Aperture, when we used iTunes to sync the albums. The users want the photos to be sorted in a specific way, but the developer team does not seem to have the necessity high on the list of requirements to preserve the sort order in an album .
For a short time there has also been a Support document explaining, that the photos will be synced with iTunes to the mobile devices, but not the sort order in the albums - this document has been removed and I can only find out on the wayback machine:(https://support.apple.com/de-de/HT4221).
Some background information in this discussion: When will iTunes Photo sync order be fixed - Apple Community
Over the years I have seen variations on these statements on the sort order:
iOS: Understanding photo sorting
The order in which photos synced from your computer are sorted in the photo albums of your iPhone, iPad, or iPod touch depends on the software you are using on your computer. Learn how this works in iPhoto, Aperture, and other software.
By default, photos sort according to the date modified (in ascending order).
When syncing photos from a Mac or PC, some apps may sort your photos in the order you specify in the app (such as iPhoto or Aperture). If your app does not support this feature, photos will be sorted by the date modified.
In addition to albums and events, synced photos appear in a unified category called Photo Library (on iPad, this is the Photos tab). Photos are not duplicated. This category will also sort photos in ascending order by the date modified.
Additional Information
If you are using an earlier version of iOS
iOS 4 sorts photos by the Date Taken tag of the photos. iOS 3.1.3 and earlier sort photos alphanumerically by the photos' file names.
None of Apple's current support documents is promising that synced photos in albums will arrive in the same order as in the source album. If they do, it is probably an unsupported feature that can break any time.
Even within a Photos Library the sort order of the photos in an album can get lost, when we add photos to a project for a slideshow or to a shared album. Albums seem to be treated mostly as unordered sets of photos and videos, not as an ordered sequence of photos.
I can understand this, because it is a daunting task, having to sync consistently between many different platforms running different system versions.