It depends: there is a range of stimulatory and inhibitory effects of substrate micro-organisms on germination. So you need to know the requirements of the specific seed before germination. For example, germination of wheat seeds inoculated with bacteria (Effective Micro-organisms, EM) was either stimulated, or inhibited or remained at control levels depending on the amount of EM. So you need to select your medium (soil versus culture medium) based on these criteria :)
See:
Adv Space Res. 2001; 27(9):1611–5.
Effect of bacterial population density on germination wheat seeds and dynamics of simple artificial ecosystems.
actually we can't grow artificially produced seeds directly in soils, bcz we requiers sterile media for culturing these type of seeds but we can use mixture of propagating media with soil.
To avoid inconsistency of encapsulated embryo we should check its conversion response to shoot and root development..this we can do under aseptic conditions afterwards we can go for green house directly