I think for me, the main takeaway from article is startup time for JITs is irrelevant, since it does not affect performance much.
First, the JIT compiler has often done most of its work during the first in-process iteration, so the plots are not generally following a "one in-process iteration is slow, then the JIT kicks in from in-process iteration 2 onwards" model. Put another way, the JIT compiler is often making even the first in-process iteration run pretty fast.
Second, I would suggest that the often small timing differences are more worrying than they may first appear. In a semi-mature compiler, optimisations are frequently in the range of a 0.5-1% improvement. So if your measurements are only accurate to (say) 2%, most of your attempted optimisations will be misclassified (bad optimisations will sometimes be measured as good; good optimisations will sometimes be measured as bad). Furthermore, when a VM recompiles things, it generally performs several optimisations at once. Thus, if the overall performance gets worse (even if by a small bit), it may suggest that several optimisations performed badly at the same time.