Well, Jackpot, what you and the pulse boat player are doing is likely to be something pretty common, going through various phases most BT players go through. It is hard for a new player to pass up the apparently awesome combination of pulse lasers and targeting computers, even with TW rules where the pulse lasers cannot use the targeting computer to make aimed shots. A big -3 to hit is rather enticing, so you cannot really blame the new guy.
You pointed out your own customization phase, which is to try and hedge your bets by padding your mechs' critical locations with stuff you wouldn't mind using, such as a small laser. When you look at the game from the point of view of someone playing a game it makes sense to try and pad those critical locations, but if you were a weapon designer in the BT universe you wouldn't likely slap a small laser on the head of every mech you designed. The small laser would actually bulk up the size of the head, which would make it an easier target.
The stock designs have, for most of the game's history, attempted to take a balanced approach towards the weapons mix and positioning of such. If you look at a lot of the 3025/3039 designs you'll start to see a lot of machine guns and flamethrowers, but as you get to the later tech readouts many of those AI weapons have been dropped. Part of the reasoning for that is er small lasers were doing 3 points of damage to infantry and had better ranges then MGs and flamethrowers, making it a compromise. Now with TW rules those er small lasers are worthless against infantry, and the need for MGs and flamers have come back. A lot of new players want to just play "mech only" games, which leads to customs missing those AI weapons.
I would say that your padding of components via custom variants is on par with the new guy with targeting computers and pulse lasers. One could say that one is more "new" then the other, but both are pretty "new" things to do. At the same time both are valid moves and used by those that have played the game longer. What balances out what your friend is doing is his units' BV2 scores. He is paying for his pulse+TC combo with points, but what you are doing is something that is effectively free. Last I checked there wasn't a difference in the BV2 value of a mech that puts a small laser that is in the arm to start, into the head to pad the pilot. This means that your friend could point to you and say that you are seriously gaming the system.
Customs are allowed at the table nowadays, just as they were back in the days in the games that I have played. Some of the people are different, and so is the force selection. Where 2 friends that used to be around always used customs, the new person to the group seems to use forces that are made up of stock designs, but also does not use proxies. This is much closer to what I and another guy have always done, which is to use I.S. stock designs with very few changes. If someone else joined the group and brought all custom designs, as long as those designs were validated for BV2 scores, and tech, and they let us know what each design was, theres no problem.
Things seem to change as you play the game longer. I have gone from using nothing but proxies and always making a few tweaks to the designs used, and using any design that happened to be I.S., or Clan, depending on what I was playing, to more faction based forces. Also, I have started painting minis in specific unit paint schemes. It takes far more time to design a force then before, but its another challenge to the game, especially when that starts to influence the minis that you purchase. I have been picking units I like for some reason, some to fill out the units I am building; and some designs that I don't really care much for, but are either solid designs of a faction, or fill out units nicely such as a locust. What it comes down to is finding different aspects of the game and learning it, having fun with the challenge of it, and then finding other aspects. Its a matter of time before you and your friend move into different phases.
