S asks:
Abaye answers (just before second Mishna 98b) that we are talking about a large ziz (ledge) which is under a smaller ziz of less than 4 tefochim - hence a mokom petur.
How can there be a mekom petur in the domain of a reshus hayochid (which continues 'ad hooray) ?
S,
The Kollel replies:
The Hagahos ha'Gra skips the words "Makom Petur" (although Rashi does call it Makom Petur). An expert in Eruvin suggested to me that even though, normally, everything above remains Reshus ha'Yachid, here -- since the lower Ziz has no real walls -- Gud Asik to continue the "walls" higher does not apply (according to Rashi).
All the best,
Reuven Weiner