Hi Tony,
I'd prefer you to see my comments as observation or even to see them as light criticisms tempered by experience with other products in the same class rather than a whim, hunch or without logical reason. I've shot 1dx's , A7rii, A7s, A7ii and Pentax K1 bodies over the past few years (currently with XT2 and 1dxii).
It's quite possible (and reasonable) to suggest that Sony's engineering has allowed for a perfect seal when the audio input flaps are closed and that they simply do not need to include grommets/gaskets. Comparing with Canon and Nikons approach where liberal usage of rubber flaps and rubber grommets around audio input jacks on the 1dx and d5 and this design choice has already proven itself over a number of camera body generations to be effective in providing class leading weather sealing. To answer your question I'd personally prefer to have rubber flaps and gaskets around any area where water/dust could ingress
Take a look at Roger Cigala's tear down of the Canon 7d ii to get an idea of the level of sealing the competition puts into their camera bodies (lower cost APSC in this case). This level of sealing does not necessarily incur a significant size/weight penalty either.
There are some interesting observations on the 7dii teardown, notably that liberal usage of rubber grommets in a camera body design really does help prevent dust/moisture around ingress points rather than relying only on tight fit and finish

While I don't normally like sharing petapixel articles - of late I've found them quite sensational rather than fact based or informative, I do really value the opinion of Roger Cigala (guest author here). He runs lensrentals and has taken apart/repaired any number of camera bodies and lenses.
Cracking Open the 7D Mark II, The Most Thoroughly Weather Sealed Camera I've Ever Seen
Zeiss also tend to believe that rubber gaskets are a good thing in their weather sealed lens lineups.... (note the mentions of gaskets)
Whatever the weather
Again let's wait and see, even if the A9 is not as weather sealed as the D5 or 1dx, this does not make it a bad camera particularly if you do not care or need good weather sealing for the environments in which you shoot. Somebody will no doubt give their shiney new A9 a dust and water bath... like this guy!!!