In response to a few of the above comments:
"One can certanly cut it off" - Actually, that is not correct. Once the tefillin are worn for the mitzvah they become kadosh and can't be discarded unnecessarily. If the blackening of the retzuah will hold for some time (I'd say a few months) then they should not be cut. However, if you'll have to regularly touch them up then the piece should be cut off and put in shaimos.
Black shoe dye (not to be confused with polish) likely is made with synthetic ingredients. If so, it may be used to blacken retzuos. (The black pigment could be sourced from burnt bone, which could include non kosher animal species.) It is inappropriate to use the same bottle of shoe dye for shoes hence, either way, one should invest in paint specially for tefillin.
It is not necessary to use a utility knife. A quality pair of scissors works just fine. (25 years and countless meters of retzuos have proven this.)
The retzuos are cut on an angle at the end because it is easier to get them through the passageway and easier to knot. Once finished they are usually left this way. Perhaps some cut the end a special way as a means of differentiating between Rashi and Rabbeinu Tam.