I tried matrix bridged to IRC (libera) a while ago. It didn't sync back to matrix properly when people on irc left the channel, so you'd try to talk to someone on irc who wasn't there anymore. One time, a person on irc couldn't see any messages by any matrix users until they reconnected to the Network. And IRC is an old, open, well understood protocol. I just cannot imagine that a bridge to eg Whatsapp would result in anything even remotely usable.
To be fair your first problem sounds like an impedance mismatch more than anything else. Users come and go from IRC all the time because connections are transient by nature. It would probably be annoying to a lot of people if they left the room every time they disconnected.
Matrix and WhatsApp are both durable with regards to users so this issue probably isn't relevant.
Personally I find the biggest problem with puppeting is the impedance mismatches. For example if reactions aren't bridged it can be easy to miss stuff. This depends on the bridge used.
This is honestly the problem with a lot of these type of FOSS replacement products. It's not an "impedance mismatch" and the user isn't "holding it wrong", the product has bugs. They need to be acknowledged as the bugs they are and addressed, because the fact is of you want to replace a product you need to not be worse than that product.
