Lets examine the differences in order to get the answer (or skip straight to the bottom for the quick version!).
Size – An 18650 battery is 18mm wide and 65mm long. A CR123, CR123A or RCR123 (a rechargeable variant of the normal CR123 like our Eagtac version) is 16=17mm wide and 35mm long. Putting two of these together leaves you 1-2mm short in width which isn’t a huge problem, but it also puts you at almost 5mm longer and this can be a problem. A device designed to use two CR123 cells will allow for this. A device designed to take an 18650 might not. Forcing the cap onto a torch designed for an 18650 for example may crush the positive button tops on a CR123, or crush internal components leading to a short circuit and potentially a fire/explosion. Likewise, a device designed to take two CR123/RCR123 batteries might accept an 18650 in physical size, but the output of the device may be poor (in the case of torches/flashlights) or may not work at all if it requires more than 4.5V to operate.
Capacity – Typical capacities for CR123/RCR123 cells range from 700mAh to around 1500mAh per cell/battery although they’re normally around the 1000mAh mark. 18650 batteries are available anywhere up to 3500mAh per cell/battery. If your device is designed to take an 18650 battery, you’re actually doing yourself a disservice using CR123/RCR123 cells instead, by having less available capacity. Putting two 1500mAh CR123/RCR123 cells into a torch/other device doesn’t give you 3000mAh because you’re putting them in in series, i.e., positive to negative. You can only increase capacity with parallel connection.
Voltage – Touched on briefly above but we’ll open it up here – Series Vs Parallel connection. Connecting batteries in series increases voltage, adding them together. The nominal voltage of an 18650 battery is in almost all cases, 3.6V. A non-rechargeable lithium CR123a is 3.0v and an RCR123 (rechargeable lithium-ion) is 3.6V. Using two CR123/RCR123 in series (one stacked on top of the other) therefore increases the voltage to 6v and 7.2v respectively. Your product might not be designed for this. Likewise, a device designed to take two CR123/RCR123 batteries might not work correctly at the lower voltage supplied by a single 18650.