So I decided to do the right thing and go and ask Rabbi Friedlander directly (he is very accessible, he answers in הלכות סת"ם three times a week in Yerushlaim and once a week in Bet Shemesh). I recorded with my cell phone and planed to transcribe the whole thing later, but apparently my Nokia c2-01 in a piece of junk and the recording came out very noisy and unclear, so I'll just write out the points from memory and what I managed to understand from the recording.
So in short what Rabbi Friedlander says is that when it comes to ARI Teffilin then yes indeed one is to be very makpid on the ראשי שיטין and if not, the terminology he used was "a מום in the מקח", and "it could be a מקח טעות".
Is the Tefillin mehudar? No the tefillin is definitely NOT Mehudar but it would be difficult to say exactly what level it would be, somewhere between בדיעבד and לכתחילה.
This is more or less what Rabbi Friedlander said.
Now while we are in this topic let us see what other sofrim (that know what they are doing) did. Here we see an example from R' Reuven where he streched out the וחרה and left very large gaps between the words (5 yudim between וחרה and אף!) in order to get it correct:
However if it was not important to keep the ראשי שיטין and it would be unacceptable to strech the letters, why did he not write regular?
Example 2: Why this:
(Stop! I know what you want to ask. The answer is - I don't know!).
And about this one (R' Tzvi the Baal Shem Tov's Sofer) I have nothing what to say:
(From R' Moishe's blog, all rights belong to R' Eliyahu Getz).
So as we see, in ARI Tefillin (as well as A"R) one MUST be very makpid on the ראשי שיטין. If not then it is on a (very) low level and not at all "Mehudar". If paid high price then definitely a מקח טעות.
Comments are welcome.