Thank you very much for your valuable feedback. 
Just to make sure, this would be alright:

--------------------------------------
|       SMALLER PCB       |
--------------------------------------
   )¤¤¤(      )¤¤¤(      )¤¤¤(
----------------------------------------------
|          LARGER PCB              |
----------------------------------------------

the shorter PCB above the longer one connected by mouse bite tabs?

Oh, and since I will be ordering a stencil along with the PCBs, while 
googling something related to it, I found this: 
https://learn.adafruit.com/smt-manufacturing/laser-cut-stencils

The only thing I find interesting is where they suggest to make 
modifications to the gerbers in order to shrink the size of the SMD pads: 
"You'll 
now see that your pads are thinner. This prevents bridging since the laser 
is not perfectly precise and tends to 'go over' the boundaries by a few 
mils."
Is it really needed? I have some QFN components with small pitch between 
pads, I will be ordering the electropolished stencil for added precision. 

Dana subota, 9. prosinca 2017. u 22:36:39 UTC+1, korisnik Allen Dutra 
napisao je:
>
> Hi Luka,
>
> You are correct. Everyone that I've ever talked to, looks at that mess of 
> board outlines you've circled and says "Mouse Bite". Ultimately any board 
> outline is provided to a CNC technician and *interpreted *to create tool 
> routing. Tool routing that is offset from the board outline by the drill 
> radius and concave acute angles rounded. Often a good PCB Fabricator (fab 
> shop) will point out areas that can't be CNC routed and work with the 
> customer on a solution.
>
> Take way: board outlines and mouse bites are always interpreted by a 
> technician to make sure the CNC routing works correctly. I've yet to see 
> mouse bites done incorrectly though I've have seen the drill size, spacing, 
> and count adjusted based on board thickness. If your building a thinner 
> than standard boards a fab shop may adjust the mouse bite specification for 
> reliability. Translation, make sure the mouse bite doesn't break in the 
> factory but can be snapped latter by the customer.
>
> Done correctly you shouldn't need cutting tools to snap mouse bites.
>
> Allen
>
> On Sat, Dec 9, 2017 at 5:26 AM, Luka C <[email protected] 
> <javascript:>> wrote:
>
>> @Allen I'm planning on assembling them "by hand", manually pick and place 
>> SMD components and bake them inside a reflow oven. I guess I'll try 
>> following the Dangerous Prototyping post today.
>> The only thing I do not understand is the part I've marked in yellow on 
>> the picture here: https://i.imgur.com/HmpFPwv.jpg
>> Those break tabs contain outlines of both the first and the second board 
>> as well as the arc. I suppose the technician at the fab house then alters 
>> this in a way that the machine only cuts the arcs and not the board outline 
>> directly around it as it would cut the two boards apart?
>>
>> @gregebert I'm was thinking about cutting them with something like that 
>> indeed, I'd just like to make it easier by having empty space between them 
>> and having mousebites to simplify cutting them apart.
>>
>> Dana subota, 9. prosinca 2017. u 04:17:25 UTC+1, korisnik Allen Dutra 
>> napisao je:
>>>
>>> Hi Luka,
>>>
>>> Allen Dutra, professional PCB designer currently working for Apple and 
>>> with a lot of first hand experience with PCB panels.
>>>
>>> In your case you want to use mouse bites to combine two different sized 
>>> rectangles. V-Scores won't work here. The mouse bite instructions from 
>>> dangerous prototypes will work well for standard 0.064" designs. Question, 
>>> are you soldering these boards by hand or having them built on an assembly 
>>> line? (I could guess your answer but no assumptions from me) Assembly lines 
>>> will want tooling rails 
>>> <https://www.pcbuniverse.com/articles/Tooling%20Rails,%20Holes%20and%20Fiducials.png>
>>>  
>>> for best results but these are easily forgotten.
>>>
>>> I haven't use the PCB Panelizer tool that you linked to. Generally I 
>>> design my panel in the ECAD tool (Eagle CAD, Allegro, Altium etc.) I'm 
>>> already using to ensure Gerber accuracy.
>>>  
>>> Let me know if you have other questions,
>>>
>>> Allen
>>>
>>> On Friday, December 8, 2017 at 5:07:06 PM UTC-8, Luka C wrote:
>>>
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