I'm not familiar with the Kowalski simulator or its built-in assembler, but the usual output of assemblers is a hex file, whether Intel Hex, Motorola S19 format, or something like that, which are text files with things at the beginning of each line telling what kind of line it is, the beginning address, and having a checksum at the end, etc..

ca65 puts out straight binary if told to do so, and does so in a variety of binary formats, including Commodore PRG format as well as o65.