I don't think there are many variations of the transporter strategy, or they all produce similar results of success. All I do is just unlock III bombers straight on, then from then whatever I need (usually II eco station).
My procedure, from mid to late game is:
1) Have nice blob of death near the wormhole leading to the soon-to-be annihilated planet; MRS and leech/parasites are fun, along with starships to boost attack, mainly to catch the furious wrist-cutting AI fleet.
2) Load III/IV bombers and a few fleet starships into transport (include parasites/leech for creation of distractions for ion cannons/etc. and general giggles), include lots of beer and stereotypical projections of women.
3) Send trojan to enemy command station, unload. Destroy the command station before anything else to tell the AI to make nice with nice blob of death waiting on the other side of the wormhole. Quickly destroy affecting tractor beams in vicinity, then reload into transport. Try to beat the forming AI forces over your friendly wormhole before they release BERSERKER BARRAGE on your planet; unload units back to the nice blob of death for immediate repairs and to amplify defense fleet.
3a) If there are any other important structures to destroy, such as mass drivers and fortresses, then send transport that way. The AI may at first be attacking your bombers, but they will immediately incur amnesia when you recollect them with the transport. Fortresses won't be of much hassle, honestly as a only a few volleys are needed to destroy it.
4) Wait for the AI to make nice with you.
5)
?
6) Profit! You may experience the following, a) sudden increase in fleet (or trade-off of lower tier ships to higher tier if enemy planet was such); spend less overall on your fleet (unless you are still building ships when you know you can acquire them through leeching), b) AI has escaped and is beginning spamming TIGER, TIGER, TIGER!! and TIGER UPPERCUT on your harvesters and possibly at your command station if you don't creep with your forcefields [then move on to your next planets, bad news especially if you have nothing on them]. Best if you don't allow the AI ships to pass your nice blob of death, or use engine damaging units to deal with escapees. Important that your fleet be in a single area so as to have concentrated and focused fire, along with MRS and starfleet assistance.
7) If the planet has some problematic structures that can be captured (ie. ion cannon), send your main fleet in after you have OMNOMNOM'd the enemy scourge after you have built a colony ship. I usually have a control group of engineers speed up the construction. Deploy colony ship near your wormhole (or somewhere else safe), and use engineers to immediately assist. Costs no resources (that I know) and gains constant HP so survivability increases (construction cannot be disrupted by weapons fire).
Once captured, FRD or attack-move remnants. Ion cannons can help clean up if they are able to 1HKO turrets; at this point you should proclaim, "you are on the way to destruction." Scout next planet, send taunting message "you have to chance to survive make your time" "ha ha ha ha....", then follow procedure to inspire bomber pilots to take off every ZIG for great justice once again, afterward turning to your main fleet and yell, "OUR ARROWS/weapons WILL BLOT OUT THE SUN/wormhole" as you await applause at your completely original speech.
TL;DR; main fleet to cover wormhole on your side while you transport ~200 bombers and misc. to destroy command station and other important structures. Much easier than to face both defenses and AI ships (and then have AI forces pillaging on your own planet).
I don't think you can do without transports unless you're Rambo. =\