A minilab extruder will be far less sophisticated than the real thing, and therefore there will be less parameters to be controlled for optimizing your material (such as different temperature zones, indeed). Mini extruders are only useful when you are not able to produce high amounts of materials, as normal extruders indeed require to be fed by several hundreds of grams (if not kilograms) of material, and this is often not possible at the R&D scale.
According to www.thermoscientific.com (accessed on 11/7/14), Minilab micro-compounder provides precisely controlled reactive extrusion of high viscous melts using only a sample amount of 5 grams or 7 cm^3. The micro-compounder is ideal for compounding expensive or small scale materials such as nano-composites, bio-polymers or pharmaceuticals. Therefore, the micro-compounders are very suitable for laboratories.
According to www.wikipedia.org (accessed on 11/7/14), 'traditional' plastic extruders are used in high volume manufacturing process in which raw plastic material is melted and formed into a continuous profile. Therefore, 'traditional' extruders are suitable for manufacturing items such as pipe/tubing, weather stripping, fencing, deck railings, window frames, plastic films and sheeting, thermoplastic coatings, and wire insulation.
If it is a thermoset plastic, the extrusion process is similar in both cases. A laboratory extruder will allow us to know more about the suitability of a given material to be processed at an industrial level and therefore know the parameters of work(temperatures, pressures of processing, production and consumption) and the physical properties of the plastic main (density, viscosity, fluency..) you can learn in a laboratory extruder for later use in industrial extruder.
If you mention about polymer compounding issues and a micro-compounder (vertically and horizontally designed mini compounder with conical screws) as minilab extruder, in my opinion, there are some critical differences between these devices (compounder and extruder), certainly, besides the amount of material in processing. Both are, of course, melt processing equipment but minilab(s) include non-intermeshing conical screws and recirculation channel while a twin screw compounding extruders generally have intermeshing screws that contain various types of special mixing/kneading zones (segments), specifically designed for intensive mixing and/or dispersion works. Minilabs do not have such segments. A multi-component material could be processed in a mini-compounder for many cycles to increase the dispersion (or homogenization) but thermal issues should be taken into account. A small scale extruder might be more similar to the industrial scale extruders. But, I think there is a huge gap between the processing conditions and rheological behavior of a material in a minilab and a traditional extruder, especially for thermoplastics.