It's basically it. Aggregate speed to a website is different from a file transfer. It depends upon the number of components required to be individually downloaded (html, css, javascript, images), each of which has it's own additional latency if not asynchronously accessed. A single file transfer has only the initial latency to deal with so the impact on overall perceived speed isn't as noticable.
Places like testmy operate with a single file transfer when evaluating speed. I have no idea what they do to evaluate latency, but it seems that lag times appear to be over-exaggerated, indicating that they may be compounding in some instances.
Regarding ping: It only gives you an idea of overall latency to one destination point only, inclusive of the path it takes. It's kind of limiting as a diagnostic, because you have no idea where the problem is.
Traceroute tells you:
1. Latency through the gateway - what's only attributable to HughesNet - which is usually a 4-hop thing.
2. Who your gateway provider is - usually a source of high, erratic latency depending upon who it is.
3. The route the provider prescribed, how many hops it's taking, and which hops along that route have the biggest latency problems.
So it gives you a better indication of where problems may be.