How can there be a problem with the supplied gas? The plant is...

How can there be a problem with the supplied gas? The plant is designed for the supplied gas. The gas isn't designed for the supplied plant. Simple as that. This is a design issue.
I think you are reading the Phase 2 statement incorrectly. I take it as Phase 1 being construction and commissioning of the plant to the initial plans. The problem with Phase 1 is foaming in the absorbers. Their solution (hopefully) is Phase 2 construction / remediation of the absorbers to a new plan - a parallel arrangement.
Not only is COE waiving their right to any further LDs and offering to share costs for any remediation, they are also offering to share any revenue for gas sold at spot prices. So that's going to sting them even further. But, as @AustinNZ said above, what choice has COE got left? At least by being directly involved in the commissioning, rather than getting second hand information from APA, COE will be able to keep the pressure on and get the OGPP up to it's nameplate capacity.
Maybe they should stop faffing about, leave the two existing absorbers in series, and add a new parallel branch with two more absorbers. Hell, add multiple parallel branches and just get the bloody thing up to speed.

IMO