According to the phd thesis Implementation and Assessment of
Modern Host-based Multipath Solutions of MPTCP developer Sebastien Barre the congestion control replaces traditional TCP congestion control, since the MPTCP congestion control was designed with the following principle:
“in multipath scenarios, to use only the less congested paths instead of spreading
the traffic equally among the available paths”
and he states
"Another important difference between Multipath TCP and regular TCP is the
congestion control scheme. Multipath TCP cannot use the standard TCP control
scheme without being unfair to normal TCP flows."
MPTCP congestion control distributes the throughput to the TCP subflows by altering the congestion window, which would break traditional TCP congestion control if they ran concurrently, so I believe they do not run "duplicatedly together"