Yep, that's a very valid concern, and one of the things we plan to address in a more technical post, as mentioned at the end of the current post. There are other posts which also tackle this topic, such as Ryan Sleevi's Path Building Showdown. Your analysis is good.
This is one of the reasons that we will still be supplying the EE <-- R3 <-- ISRG Root X1 chain as an alternate, and working with ACME client developers to ensure that their clients can be configured to select that alternate. Subscribers who value compatibility with older versions of OpenSSL and GnuTLS over compatibility with older versions of Android will be able to use the alternate chain to get the compatibility they need.
We believe that compatibility with older Android devices is the higher priority here. It matches up with our mission to support end users: not just subscribers/sites, but users of the Internet who may have little to no control over what device they use to browse. Also, maintainers of sites whose clients are using OpenSSL and GnuTLS are more likely to have the technical know-how to configure alternate certificate chains. We thought about this choice for a long time, and while we love the idea of serving the shorter more efficient chain by default, we don't currently think that's the right call.
We'll be thinking -- and talking publicly -- about this more in the future. Thanks to this cross-sign, we'll be able to provide chains that work for both of these use-cases. If our prioritization turns out to be incorrect, it will be easy for us to switch which chain we provide by default.