Though if 46GB is allocated to the system partitions rooting won't change that (repartitioning is something you consider at your own risk!).
That is, if 46 GB are really allocated for that. I always worry about the way that storage is presented: file sizes are normally quoted in binary, but storage device capacities are normally given in decimal units. So a '128 GB' phone (decimal) has a capacity of 119 GB (binary), and a '512 GB' one has a binary capacity of 477 GB. The difference between these 2 numbers is 9 for the smaller phone and 35 for the larger one. There's no reason I can think of why a larger capacity phone would actually need to allocate more space to the system than a smaller capacity one running the same software, so I wonder whether the apparent difference is really due to mixing of binary and decimal units? If we assume the system takes 10 GB in both cases, then the difference between the available storage and the nominal capacity would be 19 GB for the smaller phone and 45 GB for the larger one. In fact the system is the same size in both cases, and the difference is just due to mixing systems of units, but if we just assume that the difference between the total space available to the user in binary and the nominal capacity of the device in decimal is due to the space used by the system then it will appear that the system is much larger. And since Sammobile report that the 128 GB Note 9 has about 109 GB available that hypothesis would predict something pretty close to what is observed for the 512 GB Note 9.
If I'm right it's not an issue at all, just a consequence of the prefix 'G' having 2 meanings (10^9 and 2^30) which differ by 7%, and manufacturers finding it easier not to explain which is being used where.