Salaamun Alaykum.

I was reading Ayat (96:4-5)
ٱلَّذِى عَلَّمَ بِٱلْقَلَمِ
عَلَّمَ ٱلْإِنسَـٰنَ مَا لَمْ يَعْلَمْ

And I remembered that Dr. Hany explained in YT62 that there are two different عَلَّمَ in Ayat (55:2&4):

Source: [YT62; Minute 00:15:42]

The second عَلَّمَ in Ayah (55:4) is transitive, meaning it needs two object to mean "he taught":
he taught X to Y. But عَلَّمَ in Ayah (55:2) does not require an object to mean by itself “he placed markings” and thus it is intransitive and refers to the word 3alāmāt as in Ayah (16:16) عَلَـٰمَـٰت (markings);

While I was reading through Ayat (96:4-5) I recognised, that ٱلْقَلَم - the pen, is the orthographic device to point out things that remain invisible in standart Arabic - especially to the ear. Things like concatenations (Ibn Umma vs. Yabna-umma) or spelling differences like Imra'at with long To or with short Ta, or orthographic variants: words that have either a long Alif or a Dagger-Alif, but are pronounced the same, can be made clear using the pen as a highlighter.

Even the word عَلَـٰمَـٰت is written strange; instead of writing it as عَلَامَات it uses Dagger-Alifs. The word عَلَامَات is used to mean "landmarkings" - which is funny, because there are two types of such landmarkers:

1) Highlighter
2) Connector

Highlighter only exists in physical reality. While on a map (or in the memory) both can be utilised. The highlighter can be like a strange object in a forest, that stands out among the trees. It is an anomaly and allows to find it easy but also allows others to use it for orientation from there on. Sometimes if it is high or clear enough you can use it to come back to it. Like the cologne cathedral: most buildings around it are build smaller, so that you can always see the cathedral from a far to come back to the city center, where the cathedral stands. Which is useful because the main train station is located a few feet away from it. You can even see the cathedral from other cities if location allows to have a clear look on the rhine river between the cities.

On maps you can set markings using small pins and it allows you to connect informations using a thread - so that you can build up evidential, as well as unexpected connetions. In crime investigation or military intelligence, this is still a practice, and you also might know about the word "hotspots" - which serve as markings on digital maps.

So if we read عَلَّمَ بِٱلْقَلَمِ and عَلَّمَ ٱلْقُرْءَانَ - it becomes clear, that both عَلَّمَ by themselves mean “he placed markings” and are intransitive, where as عَلَّمَ in
عَلَّمَ ٱلْإِنسَـٰنَ مَا لَمْ يَعْلَمْ requires two objects: مَا لَمْ يَعْلَمْ and ٱلْإِنسَـٰنَ, likewise عَلَّمَ in عَلَّمَهُ ٱلْبَيَانَ requires two objects: ٱلْبَيَانَ and هُ .
Thus this is telling us, that عَلَـٰمَـٰت is not one specific functional tool, but a category of different functional tools, and one of those is the orthographic device, that highlights things that phonetically remain invisible. This is part of the principle of intentionality.
As already mentioned عَلَـٰمَـٰت is written strangely - pointing out that it is not just literal landmarkings, but also signs/clues, symbols and indications.
(Also عَلَـٰمَـٰت to mean landmarkings/scriptural markings adds to the definiton of ٱلْأَرْض to mean not just literal land but also scripture in the Abrahamic Locution.)

Side Note:
About concatenations I am not sure; but I have an assumption if were to consider them markings: They are indirectly serving as markings, because they may clarify and provide Bayyinat, like of Umniyyatihi vs Umniyati; where Umniyyatihi turns out to mean Um-Niyyatihi (mother of his intention i.e., the cognitive schemas, not the wishful thinking., or Salsabila to mean Sal-Sabil "Ask for (your) way". These concatenations are not always orthographic, but they stand out and makes something clear, because you can hear the difference between yy and y. Yet most people ignore it.

The word 3alam عَلَم (flag, banner) also is something to mark or make clear - for instance in ancient battlefields, the flag or banner served to distinguish allies and foes. So markings might also serve to "make clear" that what is hidden or opaque or concealed, to prevent confusion and unnecessary harm. So it might be that concatenations might also fall under the category of عَلَـٰمَـٰت .
- End of Side Note.

I also find the following marking in both Sura 96 and 55 near to عَلَّمَ بِٱلْقَلَمِ and عَلَّمَ ٱلْقُرْءَانَ :
خَلَقَ ٱلْإِنسَـٰنَ

خَلَقَ ٱلْإِنسَـٰنَ مِنْ عَلَقٍ (Ayah 96:2)
خَلَقَ ٱلْإِنسَـٰنَ (Ayah 55:3)

which links the context of عَلَّمَ بِٱلْقَلَمِ and عَلَّمَ ٱلْقُرْءَانَ in the Ayat (96:4 & 55:2) together. Meaning both intransive and transitive عَلَّمَ in these paragraphs share lessons.

What do you think of this? Do you think that عَلَـٰمَـٰت is one specific functional tool or a category of different functional tools?

Salaamun Alaykum.