Learn English – How shall the word “biology” be interpreted, if no English word can start with two stressed syllables

Why do you assume that the “underlying vowels” of these suffixes are /eɪ/ or /æ/? All of your example words are Old French or Latin in origin. In Middle English they would have been pronounced with [aː] or [a], which was later reduced to [ə].

The change from [ə] to [ɪ] has little to do with reduction, per se, but rather allophony—the sounds simply exchange in unstressed syllables for many speakers. From “Stress and vowel reduction in English”:

In some dialects of English there is a distinction between two vowel heights of reduced vowels: in addition to schwa, there is a distinct near-close central unrounded vowel [ɪ̈] (or equivalently [ɨ̞]). In the British phonetic tradition, the latter vowel is represented with the symbol /ɪ/, and in the American tradition /ɨ/. An example of a minimal pair contrasting these two reduced vowels is Rosa’s vs. roses: the a in Rosa’s is a schwa, while the e in roses (for speakers who make the distinction) is the near-close vowel.

Among speakers who make this distinction, the distributions of schwa and [ɪ̈] are quite variable, and in many cases the two are in free variation: the i in decimal, for example, may be pronounced with either sound.

This is true for all of your example words as well. Dialects where the sounds do occur in free variation are said to have the weak-vowel merger.

As Bruce Hayes (UCLA) puts it,

Word-medial voiceless stops are aspirated provided they are in the onset of a stressed syllable and are not preceded by a strident (Hayes 1995: 13).

Thus,

proton [ˈpʰɹouˌtʰɑn] in AmE.

There's no secondary stress in "voting" in AmE.

See a note on aspiration in the Longman Pronunciation Dictionary (3rd ed., Wells 2008: 45) - those rules are rather comprehensive; at least, that should be enough for someone who's not a professional phonetician.

The most important thing to remember is that aspiration is not binary, aspirated or unaspirated, but rather gradual. See fig. 6.6 in Ladefoged 2006, A Course in English Phonetics.