"The ability to throttle the compressor speed" typically (in a good unit) means it can run from rated capacity to about 1/4 rated capacity (so 48K-12K in this case) and below 12K it will turn off and on (which is less efficient than just running slower.) It does not mean that a 36K BTU unit can do 48K when needed. But the 36K unit can throttle down to 9K, typically.
IF the 48K BTU unit is right-sized, then 48K to replace it is right. That's a big if, given that oversizing of units is both common and typical (more money for the guy selling it, no complaints about it not doing the job, but more running cost, which you pay and they don't. Also has a negative impact on dehumidification.)