In East Asian Buddhism the copying of scripture is itself a practice, undertaken for merit and often dedicated to a particular purpose or person, and it was carried out on a scale that is difficult to overstate. Court-sponsored scriptoria produced canonical texts in quantity, private individuals commissioned copies, and the practice continues in Japan today under the name shakyo.
Most of that copying was of Chinese translations, in Chinese characters. Siddham enters where the untranslated material does, in the dharani and mantras embedded in the texts, in title pages and dedications, and in the sheets and charms produced for distribution, where a Sanskrit syllable might be the whole content.
The consequence for the script is that it was written by an enormous number of hands, many of them belonging to people who could not read it. A copyist reproducing a shape rather than a word makes a different class of error than one who knows what the shape says: the mistakes are visual rather than linguistic, and they compound across generations of copying, so a letter can drift a long way from its exemplar without anyone noticing.
That is one of the standing problems of the East Asian Siddham record, and it is also why the manuals and letter tables mattered so much: they were the correction against drift.