"Transplantation" sounds like a Bushism to me. "Transplant" is already a noun, thank you very much.
It's all fine until you start modifying triggers and templates. First there's the evil, kludgey combination of bad perl and bad Mason which you have to write overlays to, then once you've done this, you can't upgrade! If you upgrade, all of your overlays break. So you end up stuck with an out of date version with patch on top of patch.
Yes. If you make customizations, then you need to maintain them and update your patches to the current version.
This issue is not specific to RT. It is a fundamental issue of software development and revision control, and will affect you any time you make local customizations to software.
Perhaps you think it would be (easier|cheaper|Soviet America) if you had some shrink-wrapped proprietary software which you couldn't customize?
Why would botnet harvesting be done by domain name anyways? Wouldn't it be easier to collect systems by just running through accessible IP addresses?
RTFA. The bots are generating domain names which they then attempt to contact in order to re-connect with botnet control.
It's very clever, really. The algorithm can generate a near-endless list of domain names, and all the botnet owners have to do is register one of them and set it up to respond to the bots.
On the other hand, in order to block this attempt by the bots to re-connect with the botnet owner, you have to pre-emptively register ALL domains which the algorithm generates. So in the long run, it's not financially feasible to block this.
I assume that the researchers are now going to try to make arrangements directly with the registrars to block registration of such domains in the future -- hope they can get co-operation on this.