Asking for a better than or worse than answer is really opinion based. In my opinion it is not a good idea to use these marks to learn scales and positions. It will just turn into a handicap that will be difficult to unlearn later.
If you have to adjust your expectations when using a capo or changing guitars you are creating more mental stress and one of the points of mastering a musical instrument like the guitar is to have it become natural, muscle memory. In my experience both as a student and a teacher is that this leads to a dependency on hand eye coordination and sight reading becomes impossible.
When learning violin or upright bass for the first time it is not uncommon for the teacher to put a small piece of tape at 2 positions to help the beginner learn to get a couple notes in tune correctly. Proper hand posture should do the rest. However it is only a double check. Really the student should be using their ear. Once that develops the tape is removed (usually vary soon after starting). As for guitar, well classical guitars do not have any markings on the finger board or on the side of the neck. You are not supposed to develop a dependency on these or on hand eye coordination. Ideally your eyes should be looking forward, at the sheet music. Even my first electric guitar teacher would "encourage" me to never watch my hand. He would say "I wish they never put those makes on the neck, it screws you up".
Think about this, unless you have some type of handicap people do not look at the stairs when they walk up or down them. You have the ability to "feel" the step size. If steps are slightly off that could cause a person to fall. Well the same is true of the guitar and other instruments. There are some very simple exercises that any trained guitar teacher would give a beginner to help develop the feeling of distance on the neck. As long as you develop the correct hand posture and that distance feel you should be able to develop the ability to play with your eyes closed. This is not some advanced virtuoso type of anomaly, this is a standard (or used to be).
I suppose if you are in a stage performance situation where you are moving around and may not be able to rely on your "hand ear" coordination an occasional glance at the fret board might be necessary, but this is the exception not the rule.
In short if you rely on the markings to know where you are you will likely get screwed up if you play a guitar with different markings (some have only 5, 7, 12) while others have (3, 5, 7, 12, etc). There is no standard for how many marks to place on the guitar. Different markings can make you think you are in the wrong place. For those who might say it's okay for a beginner since they need the help and will eventually not need them (like training wheels) I would say that in this case it can be more difficult to get away from the dependency than to not have it in the first place. Guitar isn't (or shouldn't be) as dangerous as trying to ride a bike for the first time.
Based on my experience I'd resist it. If you are not taking lessons and are self learning from books and videos I'd suggest taking lessons for a while. A good teacher will know how to put you on the right path to proper development.