[RPG] Does a size large or larger creature killed by Negative Energy Flood rise as a medium sized zombie

Stat Changes

It seems very clear that you apply no stat changes.

This ability functions as a polymorph spell, the type of which is listed in the creature's description, but the creature does not adjust its ability scores (although it gains any other abilities of the creature it mimics).

There are no qualifiers here -- it says the creature does not adjust its ability scores, so it doesn't! The part of polymorph that you're looking at says that you

adjust its ability scores to one of these two sizes using the following table

This is exactly what the change self ability tells you to ignore.

Even though it doesn't use the word "adjustment" in the actual text of alter self, the word would generally mean any change to your stats. (And it would be a bit weird if shifting into a smaller form increased the strength of a Titan.)

Other abilities

There's nothing here to modify how polymorph spells work:

While under the effects of a polymorph spell, you lose all extraordinary and supernatural abilities that depend on your original form

Note the qualifier. You only lose the ability if it was contingent on your original form. In many places the DM will have to make a judgement call on whether that applies. But obviously, say, a manticore that shifts into human form can no longer use its Spikes special ability. The rule is intended to rule out nonsensical situations, so the change shape ability doesn't alter these rules at all.

If your intention is to control Large and larger undead: that's pretty easy.

If your intention is to create Large and larger undead: you will either have to wait for WotC to produce the appropriate material, or... get creative with your DM's world.

A wizard of the school of necromancy is given little restriction on their use of their Command Undead feature other than the undead's Charisma and Intelligence (Player's Handbook, pg. 119):

Starting at 14th level, you can use magic to bring undead under your control, even those created by other wizards. As an action, you can choose one undead that you can see within 60 feet of you. That creature must make a Charisma saving throw against your wizard spell save DC.

...

If the target has an Intelligence of 8 or higher, it has advantage on the saving throw. If it fails the saving throw and has an Intelligence of 12 or higher, it can repeat the saving throw at the end of every hour until it succeeds and breaks free.

Therefore, any undead you can see can be yours, as long as it is dumb and ugly enough and you are powerful enough.

Unfortunately, there are no spells or abilities published yet that allow creation of giant undead. However, if they exist in the world you inhabit, they must come from somewhere, right?

Therefore, your first task would be to find out what makes giant undead creatures in the world. Find out what is creating them and where:

• Is it an NPC necromancer who stumbled across an ancient artifact that can amplify the effects of necrotic spells (as in my campaign)?
• Is there a haunted graveyard where the restless dead can't help but stretch their legs? (common trope)
• Or is there a particularly unholy bog somewhere nearby that just imbues corpses in it with undeath?

Once you find that answer, simply harness that energy, adapt it to meet your needs, and you will be churning out giant undead slaves in no time.