The thermal voltage of a BJT, \$V_\mathrm{t}\$, is not the default voltage across a junction. It originates from the Shockley diode model from which large signal BJT models are formed:
$$
I = I_\mathrm{s} \left(\mathrm{e}^\frac{V}{N V_\mathrm{t}} - 1 \right)
$$
where Is is the saturation current, Vt the thermal voltage, and N the forward emissivity coefficient or ideality factor.
The 0.7 V you mention also can be derived from this model, which is referred to as the forward voltage, when using parameters suitable for a silicon diode (other semiconductors have different forward voltages). Typically a forward current is assumed, lets say 1 mA, which when solving the above equation for V, produces a voltage of around 0.7 V. This voltage is similar for a range of currents due to the exponential nature of the equation, which is why it is commonly stated. To try this out the parameters for a silicon pn junction are around \$ I_\mathrm{s} = 10^{-14}\ \mathrm{A}\$, \$ N = 1\$, and \$ V_\mathrm{t} = 25\ \mathrm{mV} \$.
The thermal voltage actually arises from the junction temperature, given by
$$
V_\mathrm{t} = \frac{kT}{q}
$$
where q is the charge on an electron, k is Boltzmann's constant, and T the temperature in Kelvin. For room temperature this comes out around 25 mV (depending on how hot you like your room :) ).
A BJT features two pn junctions that are typically modelled using the Shockley model, plus a bit extra. I recommend reading up on the Ebers-Moll model. The Hybrid Pi model is derived from large signal models like the Ebers-Moll model by finding the DC operating point, and from this finding the derivatives of currents with respect to voltages. The derivative of a nonlinear impedance linearises the model around a point, giving transconductances and resistances depending on which derivative is used.