This is a classic question. I'm quite surprised we didn't have a question like this already on this site. I will do my best to explain.
First of all, let's examine the actual passuk:
:וּקְשַׁרְתָּ֥ם לְא֖וֹת עַל־יָדֶ֑ךָ וְהָי֥וּ לְטֹֽטָפֹ֖ת בֵּ֥ין
And you shall bind them for a sign on your hand, and they shall be
for a reminder between your eyes.
The Hebrew word here most often translated as "between" (בֵּין) can also mean "opposite." With this in mind, we can translate the passuk as "...They shall be for a reminder opposite your eyes" and this would make more sense when we examine how tefillin are actually worn.
As you linked, the box is placed somewhere at the hairline, and not "between the eyes" on the bridge of the nose. As per Jewish Law, the tefillin shel rosh must be positioned centered between the eyes while remaining placed on the hairline. This would make them "opposite" the eyes.
The first link you brought is from a Karaite source. Karaites reject the Oral Torah and the instructions from the Rabbis and generally follow the Written Torah from a literal level. If one were to follow the Torah literally, he would place the tefillin between the eyes, on the bridge of the nose. (This would be incorrect as per Jewish Law.) But what's more interesting is that Karaites do not wear tefillin at all, they interpret this passage as non-literal, and that you do not have to literally have the words on your arm and head, but rather that the passuk means that you should constantly have the Torah on your mind and in all your actions. But we're not here to talk about what Karaites think. Let's get back to the subject.
The Gemara in Menachot 37b brings the reasoning behind placing the tefillin on the hairline:
גובה שבראש מנלן דת"ר בין עיניך זו גובה שבראש אתה אומר זו גובה שבראש או
אינו אלא בין עיניך ממש נאמר כאן בין עיניך ונאמר להלן (דברים יד, א) לא
תשימו קרחה בין עיניכם למת מה להלן בגובה שבראש מקום שעושה קרחה אף כאן
בגובה של ראש מקום שעושה קרחה
From where do we learn that the tefillin shel rosh must be on the
upper part of the head? For our Rabbis taught: "Between your eyes",
that is, the upper part of the head. You say it is the upper part of
the head, but maybe it means literally between the eyes? It is written
here: "Between your eyes", and it is written there: "Nor make any
baldness between your eyes for the dead". In the latter case it means
the upper part of the head where baldness can be made, so therefore in
the former as well it means the upper part of the head where baldness
can be made.
This the basic answer. There are many more things to say on this matter. I'd suggest reading the whole Gemara there in Menachot.