Well, I don't believe they're more physical, but I do believe they match up well against the 49ers.
They run a 4-3. Against a power run team, this formation does well. The SH have an incredibly smart coach in Carroll, and an incredibly smart secondary. 49ers run a passing attack which is designed to get a particular receiver open. 49ers depend on execution in passes, if the designated receiver isn't open (defense doesn't bite) it's a sack, throw away or Keap needs to take off. That just doesn't work against a top defense.
Their offense will over-match the 49ers defense over time. DL can only take so much direct punishment before they start to get blown off the ball, the LB's will not fair well if OL start chipping into their level.
To beat the SH, the 49ers will have to put up points. To put up points against a team that has a smart fast defense, you're going to have to reduce dependence on play-action and AR's.
There are a lot of teams that have a hard time scoring on the SH..... so, they're also doing something right.
[ Edited by Geeked on Jan 27, 2014 at 3:26 PM ]