The question relies on a number of unidentified assumptions about word boundaries, which are not totally alien but also are not obvious or obviously right. The main problem I see is the premise that there is this one thing, word boundary, that solves myriad problems.
The notion of there being a single "phonological tree" seems to be historically based on importing notions of structure from syntax (we wanted phonology to be more like syntax), but the properties of tree-like representations as used in syllable and foot structure are not the same as those employed in syntactic representations (prosodic structure is not seriously recursive in the way that syntactic trees are; phonological "trees" flout the single-mother convention). Attempting to align phonological grouping with morphosyntactic grouping just leads to tears, though that is not obvious if you consider just English. The problem is that combining a VC root with a VC prefix and a VC suffix typically leads to phonological V.C+V.C+VC, i.e. syllable boundaries seriously misaligned with morpheme boundaries.
In English and in contrast to other languages such as Arabic, there is not much evidence for resyllabification between words, so prosodic and syntactic constituency are not generally at odds. At the level of affixation, we do have mismatches involving V-initial suffixes (invite [ɪn.ˈvajʔ], invitee [ɪn.vaj.ˈtʰi]), but not at the phrasal level in e.g. "invite Igor". In asking about word boundaries in "the big house", "motorcycle" or "What are you going to do?", you have to have a theory of entities (are there both word and syllable boundaries? Are there also morpheme boundaries?), and what those entities do for you. Are there necessary or sufficient criteria for diagnosing ".", "+" or "#"?
The reason for positing word boundaries is usually syntactic: "the" is a word, it occupies a certain syntactic position, same with "big". We might claim that "motorcycle" has an internal word boundary because "motor" and "cycle" are words, and neither can reasonably be called a prefix or suffix. Phonologically speaking, there is nothing about "motorcycle" that demands a word boundary.
Certain concatenations that can be lumped together under the rubric "contraction", for example "going to" → "gonna", "will not" → "won't", "got you" → "gotcha", also "Harry's", behave phonologically more like affixational structures, even though they are syntactically more like word combinations. Just positing a readjustment of boundaries (removing the "#") does not solve all of the problems, especially in negative inflections (my analytic prejudice is now revealed).
The final complication in analyzing the aforementioned concatenations is that boundaries are also invoked to account for some facts of speech speech rhythm. The two syllables of "lighthouse" have a fixed rhythmic organization (prominence on the first syllable), but the phrase "light house" has variable rhythm (depends on whether you're shopping for a light house vs a heavy house; or is the discussion about a house that is light vs. a hose that is light). Again, attempting to reduce these speech rhythm properties to nothing more than differences in word boundaries has proven to be futile. Once you introduce some other mechanism for encoding rhythmic distinctions, manipulations of word boundaries becomes unnecessary – we can just posit that word boundaries are there if and only if we syntactically concatenate two words. You still have to have an account of whether "won't" is two syntactic words (as opposed to two syntactically-mandated functions manifested within a single word).
In other words, manipulating word boundaries has not proven to be a useful method of analysis.