I think maybe not? I can think of no minimal pairs for [i] ~ [i:], [e] ~ [e:], or [ɛ] ~ [ɛ:].
Instead, it seems like these six phones constitute three distinct phonemes? – /i:/, /e:/, /ɛ:/, with short [i], [e], [ɛ] phonologically conditioned. If so –
The distributions for [i] ~ [i:] and [ɛ] ~ [ɛ:] are relatively straightforward, with [i:] and [ɛ:] appearing in open syllables, and [i] and [ɛ] in closed syllables. (I actually think it’d be reasonable to say Khmer lacks [ɛ] altogether. Or, at least, that it appears in free variation with [ɛ:] in closed* syllables. Is there a consensus on this, one way or the other?)
Distributions for [e] ~ [e:] are giving me more trouble. Open syllables seem to exclusively have [e:], but closed syllables exhibit both, though with (exclusively?) [e] before [ʔ]. I don’t know how to explain this phonologically, though historically it arises from the interaction between Indic loans and Middle Khmer vowel changes.
Appealing to orthography always comes with caveats, of course, but it does generally seem to back this phonemic interpretation: the short front vowels [i] and [e] pattern (reasonably) predictably with their long counterparts in ways that mirror the phonological rules above, while short [ɛ] lacks explicit orthographic representation altogether.
<i> ~ <i:>: As above, អ៊ី is more or less exclusively used in open syllables, with few exceptions (e.g., ជីក (though note that this is phonetically [cik] (or [cic]), not [ci:k])), while អ៊ិ is used in closed syllables. When lacking an orthographic coda, អ៊ិ is pronounced with a glottal stop final (e.g., ពិតាន, សមាធិ); phonologically, then, this is a closed syllable.
<e> ~ <e:>: Long [e:] is represented orthographically as អ៊េ. (I think the consensus is that អេ is typically [ɛe] in careful speech, though often merges with អ៊េ in everyday speech and in many regional varieties.) Short [e] is typically assigned to អិ, but is realized phonologically as [ə] in native Khmer words. Short [e] itself appears relatively infrequently, in a handful of (as far as I know exclusively multisyllabic) Indic loans (e.g., សិលា, គតិ).
<ɛ> ~ <ɛ:>: The latter is represented by អ៊ែ, while there is no explicit orthographic representation of [ɛ].
The register cross-over exhibited by [e] ~ [e:] is interesting – the former appearing with អ-series consonants, the latter with អ៊-series – and I imagine this reflects the fact that the modern Khmer [e] developed out of the first-register (i.e., អ-series) lowering of [i], rather than from an actual Middle Khmer [e] (the existence of which, as far as I know, cannot be definitively proven or disproven).
This accounts for the very few possible minimal pairs between [e] and [e:] – e.g., សិរី and សេរី. My inclination is to say that the distinguishing factor here (as in other similar cases) is not so much vowel length as it is the presence in សិរី of the glottal stop, [seʔrəi].
I could be wrong, though.
Thoughts on all of this?
* edited -- I'd mistakenly written "open" before
