Relevant parts:
Partner represents and warrants that it shall not introduce into WhatsApp’s Systems or Infrastructure, the Sublicensed Encryption Software, or otherwise make accessible to WhatsApp any viruses or any software licensed under the General Public Licence or any similar licence (e.g. GNU Affero General Public License (AGPL), GNU General Public License (GPL), GNU Lesser General Public License (LGPL)) containing a “copyleft” requirement during performance of the Services.
Partner shall not: (i) combine Sublicensed Encryption Software with any software licensed under any version of or derivative of the GNU General Public License (e.g.; GNU Affero General Public License (AGPL), GNU General Public License (GPL), GNU Lesser General Public License (LGPL) in any manner that could cause, or could be interpreted or asserted to cause, the Sublicensed Encryption Software or any modifications to the Sublicensed Encryption Software to become subject to the terms of any version of or derivative of the GNU General Public License or other copyleft open source software
I’m not a lawyer, but under the definition of “Infrastructure” on page 5, they state that they will construe WhatsApp Infrastructure and Partner Infrastructure accordingly, which to my untrained eye is prima facie evidence to their acknowledgement that these are separate systems, at least one (the Partner’s) of which is not under their custodianship and not named as subject of the first stipulation you quoted. In other words “do not make it so WhatsApp’s own infrastructure would run GPL material” and potentially “do not send GPL material through our systems”
The second one I interpret to mean “nothing with licenses that apply that runtime operation is copy left”