The two dictionaries you cite are giving different grammatical interpretations of the string 'call/ed on someone'.
It's probably clearer to deal with the Macmillan view first. It treats 'call on' in this sense as a multi-word verb (MWV); it uses the term 'phrasal verb'. This treatment sees the 'verb + transitivising particle' as a coherent unit, a single lexeme. Here, 'on' is no longer seen as a preposition; as it is obviously an orthographic word, the term '[transitivising] particle', for want of anything better, is used. 'Call' is the simplex verb, and 'call on' the transitive MWV.
'Call on' is seen as a single-lexeme equivalent of the transitive verb 'visit'.
Jill [called on] John. ..................... S + MWVtrans + DO
On the other hand, Merriam-Webster sees this usage as verb + preposition[al phrase] (and indeed this example does fall in the grey area).
'Call' is used quite commonly in certain cases as an intransitive verb, usually 'padded' by material adding information about time and/or reason:
Jackie called to pay her respects.
Joe called on Tuesday; it was great to see him again.
Jeff called on the offchance that you'd be in and agree to see him
There is an ambiguity, in that 'called' can also mean 'rang'.
'Call round' and 'call in' are often used rather than 'call' in this sense.
According to the analysis M-W is using, with 'Jill called on John', the cohesion between 'call' and 'on' is not regarded as sufficient to call this a single lexeme (unit of meaning), so 'Jill called on John' is analysed similarly to 'Jill arrived at Paris'.
Jill called [on John]. ................. S + V + PP
So 'on' is classed as a traditional preposition.
Which is the correct interpretation? The jury is out, but personally, if there's a single-word equivalent (here: visit), I usually go with the MWV interpretation.