I'm pretty sure Unity would be able to fix this if they had their compiler always handed rounding the same way.
Also: If you want to see a sane way to handle floating point, check out the Unum format (http://en.wikipedia.org/wiki/Unum_(number_format))... higher precision than IEEE, doesn't have rounding errors, and uses fewer bits.
My takeaway: It's hard enough that I'm probably never going to attempt to implement lockstep simulation, and if I was forced to I'd probably do everything in fixed point for my own sanity.
It certainly won't provide higher precision using less bits (precision is lg(b^(l - 1)), where b is the base and l is the number of mantissa bits). For any given base, there are numbers that have no exact representation in that base (for base 10, consider 1/3 = 0.33333…, for base 2, consider 1/10), so it certainly will have rounding errors.
According to [0], the basic idea is to store the number of exponent bits, the number of mantissa bits, and the inexact bit (indicating that underflow has occured) alongside the number itself, automatically promoting/demoting mantissa and exponent as needed, and treating inexact numbers as an interval of width 1 ulp. Thus, the number of used bits depends on the number stored (which might well be less than an IEEE format would use for certain (or even the average) workload, but may very well be more due to the overhead of the tag).
[0] http://sites.ieee.org/scv-cs/files/2013/03/Right-SizingPreci...
"Finally offering a free version"
Honestly, it's been free for ages.
Not only that but Microsoft had XNA which was also a free game engine that they only discontinued last year so you're wrong thinking that html5 was the only option. I don't think you really researched the market much if you thought that.
Plus if you are serious about an RTS you should read about AI war, who used Unity. It's interesting as if you want to do multiplayer in an RTS you can't use Unity's collision detection as the float calculations are chipset dependant.