From what I've just read, that seems to be the case. We've all seen the official PC boxart which looks like it's got a DVD graphic in the bottom corner indicating the game will be shipping on a DVD disc, but it seems there's more to the DVD theory..
A fan on our San Andreas PC & Xbox forums contacted Rockstar about his pre-order through Rockstar Warehouse, and asked about the format of the game. The correspondence goes as follows:
From: Store [mailto:email@example.com]
Sent: Thursday, March 03, 2005 2:06 PM
Subject: RE: GTA San Andreas
This game will be available on June 7th. We will try to ship it a day earlier but cannot promise that we will get it in time to ship before the 7th. To answer your DVD question, the game will only be available on DVD.
Thanks for your order!
Sent: Thursday, March 03, 2005 1:56 PM
Subject: GTA San Andreas
Hi I wrote about a week ago and haven't gotten a response ... I've since then added you to my allowed senders list I had a few questions concerning my pre-order of gta san andreas I noticed on take2's uk site it says it will be released on DVD and on the North American site it says PC CD ROM and was wondering what type I will be getting I prefer it on DVD if I have a choice also I was wondering if it will shipped to arrive on june 7 or will shipping start june 7?
Don't take this as 100% sure information yet, I will send some emails around and try to get confirmation.