Why is adding gauge fixing directly different from doing so by Lagrange multiplier? For simplicity, we don't use field model.
Direct method
Consider a system $$L(x,\dot x,y,\dot y)=\frac{\dot x^2}{2}+\dot x y+\frac{(x-y)^2}{2} \tag{1} \, .$$ This system has gauge symmetry $$\delta x=f(t),\ \delta y=f(t)-\dot f(t)\tag{2}$$ for arbitrary $f(t)$. Under this transformation, $$\delta L = \frac{d}{dt}(x f+\frac{1}{2}f^2)\tag{3} \, .$$ The Euler-Lagrange equations are: \begin{align} L1 &: \quad \ddot{x}+\dot y- x+ y =0 \tag{4} \\ L2 &: \quad \dot x - x+y = 0 \, .\tag{5} \end{align} We see $$L1= \frac{d}{dt}L2+L2\tag{6}$$ so $(4)$ is not independent of $(5)$ and we need only to solve $(5)$, i.e. $$\dot x =x-y \tag{7} , .$$ We see $y(t)$ is a gauge freedom, and only fixing $y(t)$ we can solve $x(t)$.
Suppose we choose the gauge $y=0$. Then we solve $\dot x-x = 0$ with result $$x= c e^t \, .\tag{8}$$ with constant $c$ determined by initial value.
Lagrange multiplier method
Now let's try with the Lagrange multiplier method, $$L'(x,\dot x , y, \dot y, \lambda)= \frac{\dot x^2}{2}+\dot x y+\frac{(x-y)^2}{2} - \lambda y \, .\tag{9}$$ The Euler-Lagrange equations are \begin{align} \ddot{x}+\dot y- x+ y &= 0 \tag{10} \\ \dot x - x+y-\lambda &= 0 \tag{11} \\ y &= 0 \, . \tag{12} \end{align} Substituting $(12)$ into $(10,11)$ gives $$\ddot{x} - x =0 \quad \text{and} \quad \dot x-x=\lambda$$ therefore $$x = c_1 e^{-t}+c_2 e^t \longrightarrow \lambda = -2 c_1 e^{-t} \, .\tag{13}$$ It's obvious that $(13)$ is different from $(8)$.
Why do these two methods give different results?
Note: $y=0$ is a well-defined gauge condition because for any function $y(t)$ I can always choose gauge transformation $f(t)= c e^t + e^t\int_1^{t} e^{-u}y(u)du $ such that $y = 0$