Physical mitzvos sanctify the material

במדרש שאמר מרע"ה שלכך חטא המקושש כי בחול יש תפילין ובשבת אין לו ע"י מה לזכור ונתן מצות ציצית.

In the Midrash, Moshe Rabbeinu said that the wood-gatherer sinned for this reason: on a weekday there are tefillin, but on Shabbos he had nothing through which to remember — and so Hashem gave the mitzvah of tzitzis.

On weekdays a Jew wears tefillin, which serve as a constant reminder of his bond with Hashem. On Shabbos tefillin are not worn, and the wood-gatherer, lacking that reminder, came to sin. Tzitzis was given as a mitzvah that accompanies a person at all times, weekday and Shabbos alike.

וקשה כי מצות שבת הוא אות כמו תפילין.

This is difficult, for the mitzvah of Shabbos is itself a "sign" (os), just like tefillin.

The Sefas Emes objects: Shabbos is explicitly called an os, a sign between Hashem and Bnei Yisrael — so why was a further reminder needed at all?

ונראה שמצוה התלוי' במעשה גשמיי מעורר יותר האדם.

It seems that a mitzvah which is bound up with a physical act arouses a person more.

A mitzvah performed with a tangible object — like donning tefillin or wearing tzitzis — stirs the person more powerfully than an abstract holiness, because it draws him in through action.

כי קדושת שבת קביעא וקיימא.

For the kedushah of Shabbos is fixed and established (kevia vekaima).

The holiness of Shabbos is set in place by Hashem regardless of human effort; it does not depend on any deed of ours. As such it does not "arouse" a person through his own action the way a hands-on mitzvah does.

והמצות שהם במעשה האדם מביאי' קדושה גם למעשה גשמיי כמ"ש במדרש שבכל דבר יש מצוה ע"ש ע"פ ה' חפץ כו' יגדיל תורה כו'

But mitzvos that are performed through a person's own action bring kedushah even into physical activity, as the Midrash says that in every thing there is a mitzvah — see there — on the verse "Hashem desired, for the sake of His righteousness, to make the Torah great and glorious" (Yeshayahu 42:21).

Mitzvos done with physical objects sanctify the material world itself. Chazal teach that there is a mitzvah waiting to be found in every thing, so that through these commandments holiness is drawn down into ordinary, bodily acts — magnifying the reach of the Torah into all of life.

ע"כ נתן השי"ת המצות שיהיו מסייעין לאדם להמשיך קדושת התורה בכל דבר כנ"ל:

Therefore Hashem Yisborach gave the mitzvos so that they would help a person draw the kedushah of the Torah into every thing, as above.

The whole purpose of physical mitzvos like tzitzis is to give a person a means, at every moment, to channel the holiness of Torah into the material world around him — something the "fixed" sanctity of Shabbos alone does not accomplish.

Summary: Though Shabbos is itself a holy sign, its kedushah is fixed and given from Above without our action. Physical mitzvos such as tzitzis arouse a person through deed and draw the holiness of Torah down into the material world — which is why Hashem gave them to accompany us at all times.