Above is scans from book printed by Mathrubhoomi press, Calicut in 1979. Book: Dharmapadam by Thelapurathu Narayana Nampi.
This shows extensive use of dot-reph and chill-R interchangeably. There are more books which shows this same behavior. This proves that reph is treated as same as chill-R in Malayalam printing. So, as unicode decided for chillaksharams, a separate code for reph is not required.
In the scans, words marked in red-colour 1 & 2 are examples. 1 is with reph and 2 is with chill-R of same situation.
reph is equal to chill-R, only difference is the contexts in which reph is used.
While implementing reph in the font or script-engine, care should be taken to define reph in right contexts (because reph is only used in context of certain conjucts and a few consonants, not every chill-R is can be replaced by reph).
Leaving out reph is not an option at all. Having reph in a new orthography font is the choice of the font designer. But a font which claims as old orthography should include the reph, just like other conjucts. and text what shows with reph in old-orthographic-font should be readable in any font which doesnt have a reph glyph. This doesnt mean that an old spelling deprecated into new can be represented by same sequence (which involves reph).
I’m happy to be corrected if stated anything wrong above.