There is no option to stop profiling after a pre-defined amount of time. This would be tricky to use, as the overhead incurred by the tool can vary wildly, depending on the selected options and target application. Besides setting an upper limit on the number of collected results, as you’ve seen, you can instrument you application using the CUDA profiler start/stop API which is recognized by the tool. Nsight Compute has several options related to these APIs, too, in its command line guide.
Similarly, you can instrument you application or library with NVTX to specify the included or excluded ranges based on application logic, rather than on the number of CUDA kernel launches. Many DL and NVIDIA libraries already include support for NVTX.