Back then one of the most discussed minimal pairs of English was nitrate — night rate. Everyone agreed that they were distinct, despite consisting of the same phonemes in the same order. In the then dominant American ‘structuralist’ approach, the difference between the two was ascribed to ‘juncture’, or more exactly close vs. open juncture, the latter symbolized /+/. So for Trager and Smith and their followers nitrate would be analysed /náytrèyt/, but night rate as /náyt+rêyt/. (There was also the more dubious Nye trait, /náy+trêyt/.)
In LPD I indicate these same differences by the use of spacing. So I transcribe nitrate as ˈnaɪtr eɪt, while for night rate (if that were a headword) I would write ˈnaɪt reɪt, and for Nye trait ˈnaɪ treɪt. You can interpret these spaces as indicating the boundaries of morphemes or (as I chose to) of syllables.
The reason we can “hear” these junctures/boundaries is that the choice of allophones is sensitive to their presence/absence. Take another famous pair (one of Gimson’s favourites), great ape vs. grey tape. The t in great ape ˌɡreɪt ˈeɪp is a typical of t in final position: it has little or no aspiration, it causes pre-fortis clipping of the preceding eɪ; it is susceptible in BrE to becoming glottal, and in AmE to becoming voiced (‘flapped’). None of this applies to the t in grey tape (or, if you’re American, gray tape) ˌɡreɪ ˈteɪp, where the t is a typical initial one, being aspirated, not susceptible to glottalling or voicing, and not having any clipping effect on the preceding vowel.
If t and r or d and r are contiguous, i.e. have no intervening juncture, then in English they are pronounced together as a postalveolar affricate, as in train, drain, mattress, Audrey, entry, laundry. Compare what happens when they are separated, as in that rain, good reign, what result, saw drifts, ten trips, dawn drips. For more on all this, see my article setting out the syllabification principles I applied in LPD.
There are one or two exceptional cases where a putative or etymological morpheme boundary gets treated, by some speakers at least, as non-existent. I know that I do this in the word wardrobe. Although I know that etymologically it is a place for warding (keeping) robes (clothes), I pronounce its dr as an affricate, as in Audrey, not separated as in board room. Doubtless this is because I think of the word as a single item, not a compound. Personally, I do the same with beetroot and bedroom, though I am aware that some other speakers pronounce one or both of these with a boundary. I imagine that wardrobe, bedroom and beetroot are words that I knew well before I learned to read and write, and certainly well before I became aware of their etymologically compound status. (Note for Americans: in BrE a wardrobe is an everyday piece of bedroom furniture. You would probably use a 'closet' instead.)
This is what explains my different treatment in LPD of bedroom and headroom. My main prons are ˈbedr uːm, ˈhed ruːm. (Let’s ignore the irrelevant question of the vowel in -room — some people have ʊ rather than uː.) Although I ignore the boundary in the first, I think I usually preserve it in the second: headroom is a word I would not have learned before the age of nine or ten or so, and its compound nature as head plus room is fairly transparent. (Note for Americans: headroom is the BrE for ‘vertical clearance’.)
Furthermore, even when there is a boundary between t or d and r, people are not consistent in always reflecting it in their pronunciation. If I say there is no good reason to think that, I can still sometimes create an affricate out of the last consonant in good and the first in reason, even though there is an undoubted word/morpheme/syllable boundary between them. Similarly with the plosive and liquid in what rubbish!.
You may think that all this is rather good news for EFL learners. We can safely encourage them to treat all cases of tr and dr identically, namely as affricates.
But that’s to ignore people like my correspondent Jacob Chu, who has been listening carefully to the sound files that come with LPD and is dismayed by what he finds in two words we have been discussing.
The main pronunciation listed in LPD for bedroom is ˈbedr uːm. On the other hand, the main pronunciation listed for headroom is ˈhed ruːm and the pronunciation ˈhedr uːm is visibly absent, but the recording shows clearly, for British English, ˈhedr uːm. Please check the recordings from LPD. My query is, how should the discrepancy be resolved?
Beyond telling him to get a life (an idiom he might not be familiar with), what can I do but hold my hands up and congratulate him on his diligence and on the accuracy of his observations?
OK, I agree: on this occasion the actor who recorded ‘headroom’ in the studio happened to pronounce it as an exact rhyme of (my version of) ‘bedroom’. That’s life.
Of course, if I’d been in the studio monitoring the recordings (which I wasn’t, though I was for most or all of those entries in LPD that are not also in LDOCE, and also for some that are), I’d have jumped on it and got it re-recorded. Possibly. Or possibly not.