How does one prototype with SMT chips where the layout must be kept tight to avoid parasitic inductance?
What's your work environment?  Mentioning toner transfer makes me think you're a hobbyist (which is fine), but as a hobbyist you're doing this because it's fun.  Your time takes on a different value, and your budget outlook is quite different.

As a professional, I build circuit boards because it makes money for my employer.  I'm paid fairly well, and it's not economically sensible for me to mess around with toner transfer and trying to solder to that board.  I take my time and try to do it right the first time, send the boards out for manufacture, and move on to other projects.  When the boards get back, I send them through the reflow oven or have a tech solder them up (the former is easier with soldermask, the latter is easier with silkscreen and soldermask) and test.  If it works, great!  If it doesn't, I revise the board accordingly and try again.  Usually, the board works the first time, but if not, I revise it and send it out again.

Making a toner transfer board (or, at my workplace, a board cut out with a PCB router) is valuable when there's a major time crunch and you'd rather spend extra time to make sure that your prototype for the prototype works, rather than counting on the real prototype working the first time.  I'm not going to sell or mass-manufacture routed boards, and they're laid out fundamentally differently than professionally made boards:


Vias are free on professional boards, and difficult, large, and time-consuming on self-made boards
Soldering is much more difficult.  Keepaways, plane spacing, and thermals all behave very differently without soldermask.  I'll work to make soldering easy on a self-made board, but lay out a professional board differently.  
Trace/space is smaller on a professional board.  This could lead to major layout differences on some boards.  Especially with high-frequency signals, moving things closer together can change impedances and cause problems.
Some parts simply can't be soldered effectively on toner-transfer boards.  144-pin QFPs, QFN and BGA parts, and other tight layouts are far, far easier with soldermask.


In most cases, it's a better investment to send out for a few samples of the final product and wait for shipping than to do a toner transfer board as a prototype.  If you enjoy doing toner transfer stuff, enjoy getting better at soldering, and your time isn't a part of your budget (hint: It isn't, even if you're a hobbyist - you have limited time too), then toner transfer makes some sense.  If not, just get the real thing.