Pretty sure its just the pollution-generated creep, but some creep isn't collectable by the shovel.

With original Creeper it was.

Important thing to clarify: Creep can't be collected (stays on the ground) or gives zero biomass ?

Stays on the ground.

Text popup says somethin like "no creep in range".

This is not due to nearby Biter buildings.

There was a problem in Warmonger1.2.0, was fixed in 1.2.1.

And now it's giving zero biomass.

But at least I can pick it up.

But only with the tool, decon planners don't work.

Yes, zero biomass expected. Free creep -> no biomass.
Hmm, deconstruction must work. I didn't turn off that abuse. I'll check it right now.

Confirmed. Need to think about it.

I found how Factorio determines what can be mined by bots. With some collateral effect can fix deconstruction for creep 2nd type.
But I have another idea - to replace deconstruction and krastorio shovel shortcut with a special building. Such building will collect all creep in its range, store collected biomass inside. Your bots will be able to install/uninstall the building. Requires some changes in mod, but possible result seems to me more of Factorio-style than shovel/bots, that player needs some building applying special process and energy spent to clear the ground.

Oooh, that sounds really cool :)

Can I suggest a reskin of the Centrifuge for the first-pass graphics?

Balance concern: Does this mean you'll need to drag power with you to collect biomass from cleared nests?

And finally a good use for Angel's crawler MCV :-D

it'll take some time to implement. For building logics it will require energy consumption (raw fuel and then electrical versions) and pollution emission mechanics. Also correct parallel buildings work with overlapping areas needs some time. Not forgetting about priorities implementation - to remove creep under itself and other player's buildings to stop corrosion asap.
Main idea is first of all to re-invent intelligent creep collection restrictions (they are too stupid for Rampant New Enemies mode now - 64 tiles radius) and to make creep collecting not so fast operation, because enemies spent some time to deploy creep and it shouldn't be so magically easy to undo with virtual shovel.
Centrifuge is beautiful, but it has 3x3 size - not good for early game available building, and with corrosion danger 2x2 size would be better. No idea what building graphics to take (especially with license limitations every modder applied - Krastor is the only genius to share his work under GNU license as I know so far).

For now I added deconstuction support for fake creep... with collateral effect. In next version today-tomorrow. A little stupid, but no other way Factorio allows. After implementing building I'll turn off deconstruction possibility - not so fast.

I use MIT for my mods where I can if you need some boilerplate.

All entities have a value "scale" which does exactly what you want it to do to the graphics.

Also, take a look here if you want to see resized centrifuges (you want the iron_deploy_machine/"Barracks Cloning Faculity"):

https://mods.factorio.com/mod/A_Total_Automization_Illy_Varient

Centrifuges are a bit more effort than most other machines, but they look fantastic for this stuff.

Thanks for idea about graphics! I'll start with this one.

BTW I published temp fix for creep2 to be deconstructable in Warmonger update 1.2.3. With a little stupid collateral effect.