Well, there isn't an easy answer - in the lines where Black plays ...c7-c6 and ...b7-b5 he quite often follows up with ...a7-a6 and ...c6-c5 so he has to play ...a6 anyway and loses a tempo with his c-pawn ...
It should perhaps also be noted that in some lines where Black has played ...c6 he holds back on ...b5 for quite a while, playing ...Nbd7 and ...Qc7 or ...Qa5 first, in order to get White to commit!
The main problem is getting the move-order right, with White retaining the option to go for f2-f3 and g2-g4, playing a quieter approach with Ng1-f3, Bf1-d3 and a2-a4 or even going for f2-f4 with a sort of Austrian Attack.
This can be very tricky to negotiate, even for experienced professionals: in "Pirc Alert" Alburt and Chernin (I am sceptical about exactly how much input Chernin had into this book) recommend that Black plays 1.e4 d6 2.d4 Nf6 3.Nc3 g6 4.Be3 c6, but in the "Hybrid" Line as they call it, they recommend 4.Nf3 Bg7 5.Be3 a6 - leaving c6 open for the Nb8. This is fine as far as it goes, but it doesn't leave you much the wiser if White plays 4.Be3 c6 5.Nf3. Also, they recommend the following line for Black: 4.Nf3 Bg7 5.h3 0-0 6.Be3 a6 7.a4 b6 - again if White changes his move order and plays 4.Be3 c6 5.a4 then Black cannot get to this line
Do I have a solution to this? Well, if you are happy to go into a KID or an Averbakh after c2-c4, then the Modern move order is one way to go about it - this also defuses White's dangerous Bg5 lines in my view. Personally I am not so keen to do this, so I have just studied all these lines with ...c6 or ...a6 and am happy to play it either way