The dealer normally has a higher labor rate due to necessity. A dealer has many, many expenses an independent shop does not. It’s not always a given that the dealer is higher in price even with a higher per hour rate. On average a dealer may stick closer to the flat rate time book than an independent shop. An hour at 70 dollars per at the dealer or an hour and and a half at the independent shop’s 50 dollar per on the same job example.
The dealer will be more up to date on service bulletins, will have on hand many specialty tools that the independent will not, and the techs will be more familiar with various little proprietary quirks that are common to any car.
If this is in regards to the tight valve business on your Honda then simply ask them to perform a compression check. If the comp. check verifies the low compression you were told about by another shop then the valve covers should be removed and the valve lash inspected. If the lash is tight as suspected then simply ask them up front to hold off on any further repair at your expense if it leads to this. Contact the regional office of Honda Motor Co. and get them involved in this since they will be the ones paying the bill for any good will warranty situation.
Keep it courteous/professional and hopefully they will cover this for you. If they say yea then there is nothing to worry about. They will authorize the dealer to carry out the entire repair at Honda’s expense.