The original purpose of peerDependencies with npm@1 was, that a package can define packages to install alongside.
With the flattened dependencies tree with npm@3 this functionally was redundant, as ALL dependencies are getting installed alongside, as a result the automatic installation of peer dependencies was disabled and there is no real use-case for defining peer dependencies anymore..

With pnpm this isn't the case, as you choose to use a npm@1 like package dep tree, you should also use the npm@1 peerDep behaviour and install them automatically.

Say package A needs B,C,D as peerDep I would have to call:

pnpm install A B C D
# instead of
npm install A

if a peerDep conflicts with a normal dep, the normal dep should win and a warning should get printed..
(also peerDeps should get installed when linked)

What do you think?