First, do not use PuTTY. PuTTY is a GUI application intended for an interactive use. Use Plink, which is command-line/console equivalent of PuTTY intended for command automation. Being a console application, it has a standard output, which can be read in PHP (PuTTY as a GUI application does not have standard output).
With Plink, you can also specify the command on Plink command line, so you do not need to create the test.txt command file. Bluestacks Omegle
In any case, there's no way to make PuTTY or Plink separate an output of command only (at least not from a command-line).
But what you can do, is to print some header/trailer to distinguish the start and end of the command output, like:
plink.exe -ssh pi@RasPiIP -pw raspberry "echo start-of-command && command && echo end-of-command"
And then in PHP, you can look for the start-of-command and end-of-command to identify what part of Plink output is really the command output