I mean, sure, it's going to be turtles the whole way down if you're looking to define the universe without resorting to physical quantities (that is, dimensioned units). We don't have anything like a Grand Unified Theory yet, wherein we define Physics by means of some elemental mathematics (in the form that we can bootstrap computation from lambda calculus via things like the Y Combinator [0]). Besides, we occasionally give dimensional names to dimensionless quantities (my favorite being the engineering unit the inverse radian) [1]. It's a useful abstraction, and it seems confusing to complain about it.
So we resort to what we know, which is what we see. We can't see more than the surrounding universe, but we can try extrapolating from what seems to work. Attempting to stifle that inquiry seems a bit... I dunno, pointlessly antagonistic.
This article shows science in action, doing what it does best: taking observations and reconciling them with other observations via theory, and then fixing theory to match. It seems our universe follows certain equations which are themselves dimensionful, so I'm not sure why we wouldn't attempt to benchmark the universe against itself - we don't have much else to use. Even dimensionless numbers are only marginally useful, like alpha; it may "exist" and manifest as our universe, but it's not especially predictive.
[0] https://www.youtube.com/watch?v=FITJMJjASUs (one of my favorite videos - I still don't grok it, but I'm getting closer!)
[1] http://arxiv.org/pdf/1409.2794.pdf