It's warning because you overwrite the original value of
flycheck-python-pylint-executable when you call defvaralias.  In this
case you intended that, but usually it's a mistake.

You could make the warning suppression more selective by adding
(defvaralias losing-value flycheck-python-pylint-executable) and
(defvaralias losing-value flycheck-python-flake8-executable) to
warning-suppress-log-types.

Alternatively, you could do

  (setq flycheck-python-pylint-executable python-shell-interpreter)
  (defvaralias 'flycheck-python-pylint-executable 'python-shell-interpreter)
  (setq flycheck-python-flake8-executable python-shell-interpreter)
  (defvaralias 'flycheck-python-flake8-executable 'python-shell-interpreter)

(the warning doesn't trigger if the value being overwritten is `eq' to
the new one).