I used to build custom tanks, so I think I can answer your questions. Yes, you can build tanks safely so that they are just as unlikely to leak as a commercial one. However, it does take some skill, so if you are making one for the first time, I recommend starting with something fairly small.
You can make a tank as large as your imagination and budget will allow, but the water pressure it must withstand increase drastically with the size of the tank, and therefore the thickness of glass must increase also. Translation- increased cost and difficulty. As a *general* guideline, I used to use 1/2" thick glass to go up to 24" high, and 3/4" glass to go up to 36" high. Beyond that it varied:-) The biggest I ever built was 10'x3'x6' high, with 2 1/4" thick tempered & laminated front glass that weighed ~2000 lbs! The height is the most critical aspect, but the length of a panel can be an issue as well. I never built anything smaller, as it was cheaper to buy any tank (at wholesale) small enough that 2 guys could carry it than it would have been to buy the glass (at wholesale) to make it. Mark ups on tanks are not huge, so this would apply in most cases for retail as well. Something to think about.
As for silicones- GE makes lots of different silicones. The RTV series (industrial line) is used by aquarium manufacturers. It comes in clear (RTV 108) and black (RTV 103?), and several other colours as well. GE Construction series is essentially the same product (not official tested on fish but not a problem), I believe Construction 1200 is the clear version, but it's been a while. Large commercial aquaria are generally manufactured with Dow 795, which is black, but this is tougher to acquire and not generally used for small tanks. The moral of the story- colour is not the important factor. Black isn't necessarily stronger, weaker, toxic, etc. You do need to use the right silicone for the job, though.
If you have a size/design in mind, post it or email it to me and I can probably give you specific advice.