Prefixes in Slavic languages originated from the prepositions merged with the roots.
The old Slavic prepositions
подъ etc. which ended with
ъ, were merged before the fall of the reduced vowels so the vowel was kept, and you can still see it on its historical place before the roots starting with a yotized vowel: объятие.
When the reduced vowels fell, prononciation changed to agree the articulation of now adjacent consonants, but orthography did not reflect it. The words подътвердити, отъдавити (
ъ was read as a really short
ы) became подтвердить, отдавить etc, with impossible combinations of a voiced and voiceless consonant. The both consontants are now voiced or not according to the last one ([поттвердить], [оддавить]) but written the old way.
The prepositions ending in
из etc.), however, did not end with a vowel. The orthography reflected it from the beginning.
But the prefix
с- originated from the preposition
cѫ which never ended in
-с. It ended with
ѫ. This nasal sound after denasalization of the yuses had changed into
y in nouns like
сутки and into
ъ (which later fell) in verbs, and undergone the process described earlier. So this prefix does not change in writing, just as the prefixes not ending with
через (and the Church Slavonic borrowing
чрез) merged much later than the others, so until the orthography reform of 1918, they were always written