I think that when you already have helcol_three you cannot build helcol_ref. It's supposed to be either/or thing. helcol_three provides more phalangitai, reform is focused more on newer types of troops.
I've gone into EDB for that, and yeah, I see nothing that would exclude it from building if helcol_three is present. Strange, I always thought it's that way.
It's still a tradeoff that you should consider carefully especially in places with good pool of Phalangitai, as they're not included in its pool.
There is no upgrade path for Alexandreia to the helcol_ref, only Memphis.
I generally avoid Helcol_ref like the plague, because phalangitai units are beast, among the best solid heavy infantry in the game, so why anyone in their right mind would want less of that is beyond me. Especially since hammer and anvil tactics are so effective. It's just annoying how slow they are to get the battlefront compared to Thorakitai and especially the lighter, quicker Thureophoroi. Then again if you're moving your army cautiously with cavalry temporarily tucked away in the rear then making a slow advance towards the enemy isn't really a problem.
I wouldn't like it at all in terms of campaign map recruitment options, but in terms of historical accuracy it makes some sense to have the military reforms in Alexandria instead of treating it like a polis in homeland Greece. Even then, during the EBII timeframe, even mainland Greece saw the decline of the traditional Macedonian-style sarissa-wielding phalanx with the fall of Macedon to the Roman legions and soon after that the destruction of Corinth in 146 BC. Previously, in 200 BC at the Battle of Panium, the Seleucids scored a decisive victory over the Ptolemies that sent them into terminal decline with greater need for Roman aid and protection. This battle also spurred a dramatic decrease in Ptolemaic reliance on the Macedonian-style phalanx. It's probably sufficient just to have the reforms available at Memphis, with a greater emphasis on Thorakitai and Thureophoroi.