I've used 100mm travel forks on a '95 Explosif and 120mm forks on a '95 Kilauea and didn't feel that either adversely affected the handling.
The 120mm forks (Marzocchi Marathon) have ETA, so for climbing you can run them further into their travel to steepen the head angle and go to 120mm for the descents.
20mm change on axle-crown dimension alters frame angles by around 1 degree.
As I understand it, the attitude that some manufactures have towards running longer travel forks than recommended is not so much about the extra leverage that slightly longer forks will exert on the frame but more about the perceived application - ie, if you use longer travel forks you're seen as someone more likely to hit things harder and faster and drop further than someone who uses short travel or rigid forks.
This is, of course, not necessarily true and besides, how would they know what forks you were using in the event of any frame warranty issue occurring (which needn't be head tube related, of course).
You could tell them anything
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It's the same as these ratio restrictions (if they even exist) for geared hubs - how is anybody ever going to know what gearing you were using??
Anyway, there's no reason why you can't run forks further into their travel to reduce effective a/c, there's actually a lot to be said for using quite a lot of negative travel, especially on hard, loose terrain with lots of stutter bumps as it keeps the front wheel in contact with the ground for more of the time, especially during fast, loose cornering.
People often assume that a low pre-load means a low overall spring rate but it doesn't - the two are pretty much separate components of fork function and even if you run more static sag than is considered "normal" for a short-ish travel fork (ie more than 20-25%) it's still possible to set a fork or shock absorber up so that it doesn't blow through all of it's travel at the slightest provocation.
Just try it - do the usual cable tie around the stanchion thing to see how much travel you're using on a typical ride. If you're using full travel once or twice then that's fine, if less than that, then the forks could be set up to be more linear and use more of their capacity more of the time, or if they're bottoming out too much and too often then set them up to be a bit more progressive.
What forks are they BTW?
