The difference in tubing will be subtle, 725 is stronger than 631 so the wall thickness may be thiner resulting in a slight reduction in weight and a springier feel (Very subjective!) The 531 forks should also feel better than the 525, but really if you took the stickers off I doubt many would be able to tell the difference. The reason I bought the SE is the lovely stainless steel dropouts on both fork and frame, I know, how vain, though the price difference six years ago was a lot less. The SS dropouts do have a practical advantage, honest, no paint to chip and rust.
All the Cheviots are built up to order, so the standard spec is just a guide, you could have the SE spec on a Cheviot or the other way round. The SE spec shown uses slightly better components, XT mechs and hubs rather than Deore, better tyres, rack, chain, cassette... The stuff Paul recommends changes, I know that he has changed the brakes and may have changed other stuff. His website doesn't get updated often, beware the prices might be out of date, some component prices have rocketed in the last few year. If you chose either I think you'll get a great bike and just as importantly great service. Paul Hewitt is also one of the few retailers I trust, if you're on a budget he'll advise where to spend the money and where to economise. He'll also do you an incomplete bike if you already have some parts, I used an existing rack, hub dynamo and saddle, he was very fair with the pricing.