1. /rt/, /nt/
For the second and third example, I'd argue that the sonorants /r n/ are syllabic. These can in principle not appear at the beginning of a word--in English--if they are perceived as part of the nucleus of the syllable, so we transcribe e.g. Rigveda, and vriddi, or add diacrits. Likewise, with a voiced onset there's no problem:
arguably the onset can vary widely, and there should be no problem to reduce it down to a glottalic nasal, a mere opening glottal plosive
or a slow rising nasal (?)
This indistinguishable from a vowel onset, insofar both are allomorph in English!
Whereas an unvoiced nasal stop doesn't even exist, I guess, if there are no other marked features.
It's curious that you didn't mention Pterodactyl. Arguably it is not too dificult.
2. /kt/, /pl/
I would have problems with the first example, /kt-/, too, because I'm not used to any reasonable realization, and any approximation would insert voicing or at least aspiration, because my /k/ is either an approximant or a fricative (typical for Low German, I guess, with traditional /k/ > /h/, etc).
Vice versa, obstruent + liquid would always be realized with voice, so we write appl-e. The notation is simply misleading. category could be reasonably transcribed /kt-/ for certain renditions, but we still hear /kat-/ (modulo correct vowel), so this is subject to cognitive linguistics. Therefore it's not even debatale whether the inclined bilingual speaker who makes a phonemic distinction would mark the difference, if we don't intend to. I'm pretty sure it's not even close as an approximation, so that's not debatable either.
3. /h/ and the case of Ru. kto
Vice versa, Russians typically can't pronnounce /h/ and substitute a fricative /x/ instead.
kto reflects *kъto (so in Old Church Slavonic), from PIE *kwis and then some, wherein ъ "denoted an ultra-short or reduced middle rounded vowel" that is now called back yer. Today in Russian, the letter marks hard vowels that are not palatilized, but historically it could cause palatization, hence the word reflects as e.g. xto (variously), or some notable voicing in kdo (Slovenien). If it caused some form of feature in Russian that is just not phonemic in Russian it will consequently not be transcribed (therefore the specific feature doesn't matter here), much less if it's ultra short.
For some annecdotal evidence:
Perhaps the most common objection against a proposed reconstruction which
is raised time and again on general grounds, is that a linguistic form is impossible
because it does not conform to typological expectations. The classic example is
Brugmann’s reconstruction of nasalis sonans in 1876, e.g. in the first syllable of
*kmtóm ‘hundred’. Brugmann published his article in a journal of which Curtius
had made him co-editor before going on a journey. When the latter read the article
after his return, he became so enraged that he dissolved the journal and started a
new one, without Brugmann (cf. Pedersen 1962: 293). The new reconstruction
has now been part of the communis opinio for over a century.
The case of the nasalis sonans is particularly instructive because the new the-
ory soon gained general acceptance. The same cannot be said of the hypothesis
that the Indo-European proto-language had no more than a single vowel. It is
therefore important to compare the two cases in order to establish the reason for
the different treatment. Note that I am not primarily concerned with the correct-
ness of the reconstructions but with their reception by the scholarly community. If
we can find out what motivates our colleagues to agree or to disagree, it may be
possible to save a lot of time when trying to convince them.
There are two types of objection against the reconstruction of a single vowel
for Proto-Indo-European. On the one hand, it is claimed that not all of the material
can be explained from such a reconstruction. On the other hand, it is argued that
there can be no such thing as a language with no more than one vowel. Both ar-
guments have their counterparts in the reconstruction of the Proto-Indo-European
In the case of the nasalis sonans, there were two factors which rendered the
new reconstruction more palatable. While the concept of syllabic nasal was an
innovation, the syllabic liquids l and r were familiar from Czech and Sanskrit.
The new theory did not therefore affect the idea of syllabicity as a vocalic prop-
erty but only its distribution. Moreover, the class of possible reconstructed forms
was not greatly affected because Brugmann recognized, beside the zero grade vo-
calism of the syllabic resonants, a reduced grade vocalism which could be in-
voked for those instances where others might see counter-evidence. It can be ar-
gued that the real victory of the Sonantentheorie was eventually achieved by the
elimination of the reduced grade. That was a development which took much
longer than the acceptance of the nasalis sonans.
[F. Kortlandt, GENERAL LINGUISTICS AND INDO-EUROPEAN
NB: *k'mt- > **k't- was wholy rejected. (I'm sure that has something to do with the topic, but please don't ask.)