Is the difference in the spelling of some words in the Uthmanic manuscripts, in order to conform with the different readings, considered a difference in the Mushaf itself?

The differences among the Uthmanic Mushafs are of the same nature as the differences among the mutawatir (concurrently transmitted) Qira'at (readings), as the orthography follows the pronunciation, and there are mutawatir words that cannot be accommodated by a single spelling. This difference was intentional, to accommodate the general mutawatir readings, not due to error on the part of the scribes. For example, the verse: {جَنَّاتٍ تَجْرِي تَحْتَهَا الْأَنْهارُ} (Gardens beneath which rivers flow) does not accommodate the reading: {جَنَّاتٍ تَجْرِي مِنْ تَحْتِهَا الْأَنْهَارُ} (Gardens from beneath which rivers flow), which necessitated the existence of copies for each mutawatir reading.