Add --with-python=3 configure flag to replace SAGE_PYTHON3=yes

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CC:  @embray @fchapoton @mkoeppe

Component: **build: configure**

Author: **Jeroen Demeyer**

Branch: **[`8af9c37`](https://github.com/sagemath/sagetrac-mirror/commit/8af9c37152ef40a71238966e54e245ff86cd2bf3)**

Reviewer: **Erik Bray**

_Issue created by migration from https://trac.sagemath.org/ticket/24729_

