Setting paths in .zprofile or .zshrc?

It is more complicated that just a "preference". Here is the relevant section from the zsh man page:

STARTUP/SHUTDOWN FILES

Commands are first read from /etc/zshenv; this cannot be overridden. Subsequent behaviour is modified by the

RCS and GLOBAL_RCS options; the former affects all startup files, while the second only affects global

startup files (those shown here with an path starting with a /). If one of the options is unset at any

point, any subsequent startup file(s) of the corresponding type will not be read. It is also possible for a

file in $ZDOTDIR to re-enable GLOBAL_RCS. Both RCS and GLOBAL_RCS are set by default.

Commands are then read from $ZDOTDIR/.zshenv. If the shell is a login shell, commands are read from

/etc/zprofile and then $ZDOTDIR/.zprofile. Then, if the shell is interactive, commands are read from

/etc/zshrc and then $ZDOTDIR/.zshrc. Finally, if the shell is a login shell, /etc/zlogin and $ZDOTDIR/.zlo-

gin are read.

The zsh user's guide describes interactive and login shells.

In your case, this is likely both an interactive and a login shell. Therefore, both .zprofile and .zshrc are being read.

If you install Xcode 11, or the corresponding Command Line tools for Xcode 11, Apple will install a subset of Python3 into Catalina. I happen to only install Python 3 (3.8.3) from Python.org, and want nothing to do with the Apple Python3 in /usr/bin/python3. So I ensure that the Python.org path remains just as it was set during that installation.

Here is my ~/.zprofile. content. Note how I set my preferred PATH first, and then allow the Python installer to subsequently prepend their library path, so the related Python.org binaries can be found in /usr/local/bin, when I run for instance, #!/usr/bin/env python3 in a script.

export PATH="$PWD:$HOME/bin:/usr/local/bin:${PATH}"
autoload -U colors && colors
MyHost="$(/usr/sbin/networksetup -getcomputername)"
PS1="%{$fg[blue]%}${MyHost}: %~ %{$reset_color%} %% %{$fg[white]%}"
export EDITOR="/usr/bin/vim"
export HOMEBREW_NO_ANALYTICS=1
export MAXOSX_DEPLOYMENT_TARGET=$(sw_vers -productVersion)
export TK_SILENCE_DEPRECATION=1

# Setting PATH for Python 3.8
# The original version is saved in .zprofile.pysave
export PATH="/Library/Frameworks/Python.framework/Versions/3.8/bin:${PATH}"
export MANPATH="/usr/share/man:/usr/local/share/man"

alias breakpath='sep=:;print -l ${(ps.$sep.)PATH}'

export CLICOLOR=1
export LSCOLORS=cxexhxbxdxegedabagacad

and my Zsh prompt: