I'm not as familiar with gas as I spec and design primarily around electric but I've got 2 comments for you.
1. MFR recommendations for installation are usually spot on, if they show you what you want to do and you could do it you are usually ok. Make sure if you are side venting to have clearances as indicated in their instructions.
2. 95%+ of HD (and other Big Box Stores) workers are incapable of giving good advice, especially where plumbing, electric and HVAC are concerned. Most of their employees only know what someone else told them, they have no direct knowledge or experience.