Maybe one of your tubes rattled loose and unseated itself. It could also be that the contacts in the tube sockets were getting oxidized. It is not a surpize that after swapping tubes back and forth that the original tubes were fine. It can happen. In swapping out the tubes you may have cleaned the contacts enough to make a good connection again or you may have just properly seated the tubes. Before you ever buy new tubes always ensure that you have checked to make sure that your tubes are in fact bad. This includes swapping them around and reseating your tubes. Again, if your #4 tube wasn't making contact it wouldn't have lit.
I also think that if the guy at GC contradicts what Mesa tells you then I would think twice about him. Though Mesa does not approve of the Hollywood Mod and actually told their techs not to do it anymore. There are still some good reputable techs and those that will do things that Mesa says not to but most of them are not "Mesa" techs. These are the guys I would go to if not a Mesa tech. I would assume that a guy working at GC is not a good tech. A good tech wouldn't bother to work at GC.
Being that you just got those tubes I would take them back and get a refund. Really try to push the refund. If they say that you cannot get a refund for some stupid reason like they do not take tubes back as returns then I would tell them that you were not satisfied with them nor the tubes and that you would at least want a credit towards something else. Be sure that you tell them how disappointed you are with the tubes and how far you had to drive just to shop with them. Something to consider also is the color code. Compare the color code ratings of both sets. You can find information on color coding in other posts here. It may be that your set just wasn't your preference. Most of the guys at GC don't even know about the color coding or the difference in tube type by #. You can find the tube # chart posted here also if you look for it. It will explain the differences between the various preamp tubes, power tubes and rectifiers. Learn the charts if you so desire. In the long run it will help you out when considering new Mesa tubes or other manufacturers' tubes for that matter. Most good tube vendors will be able to help you out if you ask too. I would not consider GC to be a good tube vendor. They can't even tell you the difference between the tubes that Mesa grades. This is pretty poor because they are given the chart by Mesa. For that matter they can't even tell you the difference between the GT tubes either. Again, they are given a chart. Most of the people that work there are just there and that is if you are lucky to get one that is semi-conscious.
I often feel like I am talking to a wall when getting even remotely technical with anyone there. I think that it should be a prerequisite to work there that you are an absolute gear junkie along with being able to play whatever it is that you are trying to sell. I mean really, how many times have you asked a question and gotten a blank stare as if they are about to wet themselves because they can't answer your simple question and then they try to smooth things over by giving you some BS answer or change the subject. I dunno, I guess I am one of those that goes in there sometimes just to mess with them. I do buy some things there but most of the time I just tell them exactly what I want. In the case of guitars, I act like they are not even there half the time. If they bother me too much I just move or tell them to come back later. Once in a while I get a good conversation about stuff with a reasonable employee but those individuals are rare and the ones to talk to if you have a question or need information about something.
As far as not needing your rectifier tubes in SS rectifier/ silicone diode mode goes, I cannot imagine why you would need them if you never use the tube rectified mode. They are not used in the SS mode. I would however always be certain that the amp is in the proper rectifier mode selection if the rectifier tubes are not installed before I turned the amp on. If you accidentally power up in the wrong mode without the tubes you could damage your amp.