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When working with regions, you can either work with exact Region primitives, or discretized versions of the Region primitives. For example, a Cylinder object is an exact Region primitive, while using DiscretizeRegion on such an object produces the discretized version.

In general, using exact Region primitives inside of functions like RegionDifference is more difficult than using the discretized versions. With exact primitives, the output can't always be reduced to a single primitive, and so you're left with a BooleanRegion object. With the discretized versions, the output can always be reduced to a single discretized object. I recommend working with discretized versions.

Now, there were two issues with your first example. When working with inexact numbers, sometimes Mathematica is unable to determine whether the region is a valid region or is degenerate in some way. So:

DiscretizeRegion @ Hexahedron[hexpts]

DiscretizeRegion::regpnd: A non-degenerate region is expected at position 1 of DiscretizeRegion[Hexahedron[{{1.7,1.5,0},{1.7,10.8,0},{20.3,10.8,0},{20.3,1.5,0},{1.7,1.5,0.6},{1.7,10.8,0.6},{20.3,10.8,0.6},{20.3,1.5,0.6}}]].

DiscretizeRegion[ Hexahedron[{{1.7, 1.5, 0}, {1.7, 10.8, 0}, {20.3, 10.8, 0}, {20.3, 1.5, 0}, {1.7, 1.5, 0.6}, {1.7, 10.8, 0.6}, {20.3, 10.8, 0.6}, {20.3, 1.5, 0.6}}]]

Notice that DiscretizeRegion thinks that the Hexahedron object is degenerate. Your workaround was to use Round and scaling. It is much simpler to just rationalize the points:

DiscretizeRegion @ Hexahedron[Rationalize[hexpts, 0]]

(the other issue was minor. It is simpler to avoid using the Region wrapper, as it is mostly a wrapper that displays regions. So, use RegionDifference[Hexahedron[.], Cylinder[.]] instead of RegionDifference[Region @ Hexahedron[.], Region @ Cylinder[.]]).

All of your other examples will work fine with this approach. For instance, your last example (I fixed a typo where I think pts4 should have been used instead of pts3):

pts1 = Rationalize[{{1.7276, 1.47295, -0.01}, {1.7276, 10.77705, -0.01}, {20.2724,
 10.77705, -0.01}, {20.2724, 1.47295, -0.01}, {1.7276, 1.47295, 
0.6}, {1.7276, 10.77705, 0.6}, {20.2724, 10.77705, 0.6}, {20.2724,
 1.47295, 0.6}},0];

pts2 = Rationalize[{{1.7276, 1.47295, 0.6}, {1.7276, 10.77705, 0.6}, {20.2724, 
10.77705, 0.6}, {20.2724, 1.47295, 0.6}, {2.5802, 2.09795, 
1.85}, {2.5802, 10.15205, 1.85}, {19.2235, 10.15205, 
1.85}, {19.2235, 2.09795, 1.85}},0];

pts3 = Rationalize[{{1.7276, 0.47295, 0.6}, {1.7276, 11.77705, 0.6}}, 0];

pts4 = Rationalize[{{14.2533, 0.47295, 0.6}, {14.2533, 11.77705, 0.6}}, 0];

{cr1, cr2} = {2.25, 1.5};

reg1 = DiscretizeRegion[Hexahedron @ pts1];
reg2 = DiscretizeRegion[Hexahedron @ pts2];
reg3 = DiscretizeRegion[Cylinder[pts3, cr1]];
reg4 = DiscretizeRegion[Cylinder[pts4, cr2]];

reg5 = RegionDifference[
    RegionUnion[reg1, reg2],
    RegionUnion[reg3, reg4]
]