In-Reply-To headers require a redesign of the notifications package. Our recent changes improve upon the headers but can't achieve everything without an overhaul of the notifications package.
Such an overhaul would require all packages that depend on notifications to change too. Matt mentioned that he would like to further improve notifications but I don't know what his time table is.
You would need the In-Reply-To and References header, and a Message-Id generation in acs-mail-lite for a start. The latter is implemented in Mat's modified acs-mail-lite package. I and propably others are interested in this also, so if Mat can't finish it me or someone else will pick it up for sure.