This really should be the case for a set called Modern MASTERS. But apparently, the limited environment is more important than the actual constructed format that the set is supposed to support.
The design team started by listing all the cards they wanted for Constructed reasons. Many of the cards were unanimous choices... There was discussion of whether or not to reprint powerful cards from the original Modern Masters. Erik felt strongly that if the card was in need of reprinting, they should include it in the set. There was no better place to put Tarmogoyf, for example, than in Modern Masters 2015 Edition.
They started with constructed cards then built a limited set around them and the space that was left.
Given the timeline they had to work with (8th to New Phyrexia), I'd be surprised if there were many 'playable' rares that aren't included in the set. If you look at the rares that see play in Modern most of them are lands that have recently been reprinted or will soon be reprinted. Excluding those we have:
MYTHICS
- Tarmogoyf (confirmed in)
- Vendilion Clique (confirmed in)
- Dark Confidant (virtually confirmed)
- Kozilek (confirmed)
- Karn (confirmed)
- Wurmcoil Engine (status pending; was just in Commander)
- Mox Opal (confirmed in)
- Primeval Titan (confirmed in)
- Batterskull (status pending)
- Elesh Norn (status pending, probably in)
- Vedalken Shackles (was in the last one)
- Emrakul (confirmed in)
- Kiki-Jiki (was in the last one)
- Tezzeret, Agent of Bolas (sort of confirmed)
RARES
- Thoughseize (recently reprinted)
- Cryptic Command (confirmed in)
- Profane Command (confirmed in)
- Mirran Crusader (confirmed in)
- Endrek (confirmed in)
- Swans of Bryn Argoll (confirmed in)
- Scavenging Ooze? (not sure if thise counts; it was printed in commander the same year as New Phyrexia, but not in standard, and therefore modern, until a few years later).
- Splinter Twin (confirmed in)
- Grim Lavamancer? (Same deal as Scavenging Ooze)
- Inkmoth Nexus (status pending)
- Noble Hierarch (confirmed in)
- Maelstrom Pulse (probably in, since it was in the last one)
- Goblin Guide (status pending, probably in)
- Slaughter Pact (was in the last one)
- Spellskite (confirmed in)
- Blinkmoth Nexus (was in the last one)
- Arcbound Ravager (was in the last one)
- Manlands (status pending)
- Master of Etherium (status pending)
- Steel Overseer? (M11 is technically after New Phyrexia)
- Pact of Negation (was in the last one)
- Etched Champion (confirmed in)
- Summoner's Pact (was in the last one)
- Birds of Paradise (status pending, though I'd imagine not with Noble Hierarch in)
- Hivemind (status pending; I'd be surprised if this were in)
- Azusa, Lost but Seeking (status pending, but expected since it's also a commander card)
- Aether Vial (was in the last one at rare)
- Mutavault (recently reprinted)
- Blood Moon (was in the last one)
- Valakut, the Molten Pinnacle (probably in)
- Oblivion Stone (status pending)
- Scapeshift (status pending, probably in if Valakut is)
- Bloodghast (probably in)
- Engineered Explosives (was in the last one)
- Pyromancer Ascension (status pending)
- Life from the Loam (was in the last one)
- Knight of the Reliquary (was in the last one)
- Fulminator Mage (status pending)
- Damnation (status pending)
- Golgari Grave-Troll? (was unbanned after this set was developed, I think)
- Ad Nauseam (status pending)
- Living End (status pending)
- Daybreak Coronet (confirmed in)
- Kor Spiritdancer (pending, probably in)
- Bitterblossom (pending)
- Mistbind Clique (pending)
- Melira (pending)
If all of the listed cards were to be in the set, that would still leave 2 slots for rares and 1 for mythic. Some of those cards aren't likely to be reprinted for various reasons (including recent reprints, low price point, fringe playability and being past the cutoff date). There's also plenty of land cycles that deserve a reprint, which I think would be worth knocking out some fringe/low-cost playables.
I'm guessing, must like the first set, about 40% of the rares will be unplayable in constructed, but still great in limited.