A little bit of clarification:
The rules do not directly support altered NCM -- though the some of the books do recognize that some GM's use them in their home games, there is no by the book way to do them.
HD supports the rules directly, and requires custom house rules to be handled with custom templates that override the default/standard core rules.
The Race Packages in the various supplements do not take NCM into account. If a character of a given race goes over NCM then they must pay double for it by the rules. HD handles this via the Characteristics tab.
If you or your GM wants to play 100% by the letter of the rules then HD out of the box correctly and almost perfectly handles that.
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Having said that,
If you prefer that certain races are stronger or faster or dumber or uglier than others inherently then you want an alternate NCM. There are several ways of doing alt-NCMs conceptually, and HD can be made to support different ways in different fashions.
Some people like to internally balance their alt-NCM's so that if they give a race, say +3 DEX for 9 pts, they'll pay it off by generating -9 pts via lowering other characteristics (maybe -5 STR, -1 CON, -1 BOD for example).
Some people dont care about interally balancing and let the cost of the package sort itself out. They'll just raise and lower NCM as they please to model a given race.
Some people prefer that the NCM adjustment also adjust the base -- thus if the Trogdor race gets +5 STR Max, then they also get +5 STR Base -- the bar for both is moved together. Other people prefer to decouple base and max, and work out some means to reconcile differing values for both. Some people still prefer the old 4e way of doing it where a character pays for the Maxima increase seperately from base increases (even though it's mathematically unsound).
And so on.
So in short, if you want to use alt-NCM's you first have to determine what method you want to use. Once you have settled upon your method, then you can implement it in HD.
HD basically has three main methods to affect characteristics outside of NCM, with various pro's and con's.
One method is the do it yourself method. You can leave NCM off, buy stats as you like outside of NCM, and then use a custom object on one of the abilities tabs to nudge the cost of the character to where it should be via your alt-NCM method; call it "NCM Correction" or whatever suits you. If you allow points for NCM, simply and a 20 pt Custom Disad on the Disad tab. If your math is right, the overall cost of the character is correct. The pro to this is that it's easy, and anybody with a calculator can do it. The con is that it's a kludge, and requires you to do the math yourself instead of relying on HD to do it consistently for you.
Another method is via Characteristics as Powers. Since they ignore NCM, if you give someone +5 STR on the Powers tab, they will have a 15 STR, and can buy up to 20 base STR before hitting NCM and add +5 to that total. As a pro its easy, HD tracks the math, and characteristics over maxima are covered via this method. As a con you cant have negative characteristics as Powers; this is in accordance with the rules -- all Powers must cost at least 1 pt. Another con is that the base and the max cannot be decoupled via this method, if that's important to you.
The third option is to make a custom "Race" template that overrides the affected characteristics. If done correctly, this will allow HD to internally calculate your alternate NCM for a character with that Template. Its very cool. You can even override the "NCM" label to read "Trogdor NCM", or whatever as a visual reminder. The pros to this method are many, but basically all boil down to the idea that you are working with the system rather than against it -- it's an internal adjustment rather than a tacked on workaround. A con of this method is the complexity/difficulty level of making a template might be high for people without a certain level of general computing skills. Another con is file management -- you have to manage your multiple "race" custom templates yourself which might be difficult for people with poor file management skills.
As it happens, to cut down on the template creation portion of it, I made a simple asp app to do it for you, which is here:
<a target="_blank" href="http://www.killershrike.com/FantasyHERO/GreyHEROContent/RacePackageDeals/NCMExport/NCMExport.asp">Alt NCM Tool for HD</a>
The directions provided tell you how to make HD happy with the file generated by the app.
Youre on your own for the file management portion of it however.
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In summation, HD is currently tracking/allowing the packages provided in FH and other official supplements already. HD also provides the ability to either adjust it's behavior internally and allows for several workarounds as well.