Does it mean that the 1st part (the apparent ...) does not necessarily lead to the 2nd part (there is no room ...) however it leads in this case?
No, that's not the meaning here. The however emphasizes the does not mean and sets it in contrast to earlier statements, it does not negate it.
Without this sentence, the reader might come to the conclusion "that there is no room for these schemes to improve without compromising sustainability." The sentence is telling you that's not the case, despite the "apparent resilience of the current setup".
It might have made more sense to you if it were at the beginning of the sentence. This has the same meaning, roughly:
[sentences making it look like the current setup is very resilient, etc. etc.] However, the apparent resilience of the current setup does not mean that there is no room [to improve].
In other words, there is still room to improve in the current setup.